Rules and Dictionary words#

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Every word in the shipped Dictionary and every rule in the Rulebook, one entry each. Choose a tab for the core Dictionary, for one field’s pack, or for the Rulebook, and switch between a list and cards. Each entry links to its full page in the rules and Dictionary reference. Copy puts on your clipboard text that Ingence reads: how to use it.

ListCards

Core Dictionary 511 words

The words every project reads, in 12 sections. All sections

Word	Kind	Means	Pack
3D mesh `mesh_format`	format	Spelled `stl`, `obj`, `ply`	Core, formats
aborted	status	Spelled `aborted`, `cancelled`, `canceled`, `stopped`, `killed` and 1 more	Core, process
accuracy	statistic	Spelled `accuracy`, `acc`	Core, statistics
acquisition	stage	Spelled `acq`, `acquisition`, `acquired`, `capture`, `captured` and 2 more	Core, process
adenosine diphosphate	reagent	Spelled `adp`	Core, reagents
adenosine triphosphate	reagent	Spelled `atp`	Core, reagents
adjusted p value	statistic	Spelled `padj`, `qval`, `qvalue`, `fdr`, `adjusted` and 1 more	Core, statistics
administrative	file role	Spelled `invoice`, `receipt`, `order`, `quote`, `budget` and 4 more	Core, file roles
Affinity document `affinity_document`	format	Spelled `afdesign`, `afphoto`	Core, formats
afternoon	date	Spelled `pm`, `afternoon`	Core, time and versions
aligned	stage	Spelled `aligned`, `alignment`, `registered`, `registration`, `coregistered`	Core, process
ampere	unit	Spelled `A`, `amp`, `ampere`, `amps`	Core, units
amplifier	instrument	Spelled `amplifier`, `amp_rig`, `headstage`, `digitizer`, `daq` and 1 more	Core, instruments
an	connective	Spelled `an`	Core, connecting words
analysis	stage	Spelled `analysis`, `analyses`, `analysed`, `analyzed`, `analytic` and 12 more	Core, process
analysis of variance	statistic	Spelled `anova`, `manova`, `ancova`, `two-way`, `one-way`	Core, statistics
and	connective	Spelled `and`	Core, connecting words
angstrom	unit	Spelled `Å`, `angstrom`, `angstroms`	Core, units
annotated	stage	Spelled `annotated`, `annotation`, `labelled`, `labeled`, `curated`	Core, process
annotation	file role	Spelled `annotation`, `annotations`, `label`, `labels`, `roi` and 3 more	Core, file roles
april	date	Canonical `04`. Spelled `apr`, `april`	Core, time and versions
archive `archive_format`	format	Spelled `zip`, `tar`, `7z`, `rar`	Core, formats
archive helper	quality	Spelled `.part`, `.crdownload`, `.download`, `.partial`, `.tmp.download`	Core, filesystem noise
archive only	quality	Spelled `donotedit`, `readonly`, `frozen`, `locked`, `sealed`	Core, negative lexicon
area under curve	statistic	Spelled `auc`, `aupr`, `auprc`	Core, statistics
at	connective	Spelled `at`	Core, connecting words
atmosphere	unit	Spelled `atm`, `atmosphere`	Core, units
audio `audio_format`	format	Spelled `m4a`, `mp3`, `wav`, `flac`, `aac` and 1 more	Core, formats
august	date	Canonical `08`. Spelled `aug`, `august`	Core, time and versions
backup	version	Spelled `backup`, `bak`, `bkp`, `bkup`, `back-up` and 2 more	Core, time and versions
bad	quality	Spelled `bad`, `poor`, `terrible`, `awful`, `useless` and 1 more	Core, negative lexicon
balance	instrument	Spelled `balance`, `scale_instrument`, `weighing`	Core, instruments
bar	unit	Spelled `bar`	Core, units
baseline	condition	Spelled `baseline`, `t0`, `timezero`	Core, process
batch	process	Spelled `batch`, `batches`, `bulk`	Core, process
BeanShell script `beanshell_script`	format	Spelled `bsh`	Core, formats
becquerel	unit	Spelled `Bq`, `becquerel`	Core, units
benjamini hochberg	statistic	Spelled `bh`, `benjamini-hochberg`	Core, statistics
binary data `generic_binary`	format	Spelled `dat`, `raw`, `bin`	Core, formats
binned	stage	Spelled `bin`, `binned`, `binning`	Core, process
biological replicate	replicate	Spelled `bio`, `biological`, `biorep`, `br`	Core, time and versions
bit	unit	Spelled `bit`, `bits`	Core, units
bonferroni	statistic	Spelled `bonferroni`, `bonf`	Core, statistics
boxplot	file role	Spelled `boxplot`, `boxplots`, `box-plot`, `box_plot`, `box-and-whisker`	Core, file roles
broken	quality	Spelled `broken`, `broke`, `busted`, `corrupt`, `corrupted` and 2 more	Core, negative lexicon
build	version	Spelled `b`, `build`	Core, time and versions
by	connective	Spelled `by`	Core, connecting words
byte	unit	Spelled `B`, `byte`, `bytes`	Core, units
C or C++ header `c_header`	format	Spelled `h`, `hh`, `hpp`, `hxx`	Core, formats
C or C++ source `c_source`	format	Spelled `c`, `cc`, `cpp`, `cxx`	Core, formats
CAD drawing `cad_drawing`	format	Spelled `dwg`	Core, formats
CAD exchange `cad_exchange_format`	format	Spelled `igs`, `iges`, `stp`, `step`	Core, formats
calibrated	stage	Spelled `cal`, `calib`, `calibrated`, `calibration`	Core, process
calibration data	file role	Spelled `calibration`, `calib`, `cal_file`, `calibrant`, `blank_ref`	Core, file roles
calorie	unit	Spelled `cal`, `calorie`	Core, units
camera	instrument	Spelled `camera`, `cam`, `detector`, `sensor`, `ccd` and 3 more	Core, instruments
celsius	unit	Spelled `C`, `degC`, `°C`, `celsius`, `centigrade`	Core, units
centimetre	unit	Spelled `cm`, `centimetre`, `centimeter`	Core, units
centrifuge	instrument	Spelled `centrifuge`, `ultracentrifuge`, `microfuge`, `spin`	Core, instruments
certificate `certificate_format`	format	Spelled `pem`, `crt`, `cer`	Core, formats
changelog	file role	Spelled `changelog`, `changes`, `history`, `news`, `releasenotes`	Core, file roles
check	quality	Spelled `check`, `checkme`, `verify`, `confirm`, `review` and 3 more	Core, negative lexicon
checksum	process	Spelled `checksum`, `md5`, `sha1`, `sha256`, `hash` and 1 more	Core, process
chi square	statistic	Spelled `chisq`, `chisquare`, `chi-square`, `chi2`	Core, statistics
citation records `citation_format`	format	Spelled `ris`, `nbib`, `bibtex`, `enw`	Core, formats
Clojure source `clojure_source`	format	Spelled `clj`	Core, formats
clustering	statistic	Spelled `cluster`, `clusters`, `clustering`, `kmeans`, `hierarchical` and 4 more	Core, statistics
coefficient	statistic	Spelled `coef`, `coeff`, `coefficient`, `beta`, `weight`	Core, statistics
coefficient of variation	statistic	Spelled `cv`, `coefficient-of-variation`	Core, statistics
complete	status	Spelled `complete`, `completed`, `done`, `finished`, `success` and 2 more	Core, process
compressed	stage	Spelled `compressed`, `zipped`, `gzipped`, `packed`	Core, process
compressed archive	format	Spelled `tar.gz`, `tar.bz2`, `tar.xz`, `tar.zst`, `tgz` and 1 more	Core, formats
compressed stream `compression_format`	format	Spelled `gz`, `bz2`, `zst`, `lz4`	Core, formats
condition	condition	Spelled `cond`, `condition`, `conditions`	Core, process
confidence interval	statistic	Spelled `ci`, `confidence-interval`, `ci95`, `lower`, `upper` and 1 more	Core, statistics
configuration	process	Spelled `config`, `cfg`, `conf`, `settings`, `params` and 3 more	Core, process
configuration file	format	Spelled `conf`, `cnf`, `cfg`, `config`, `properties` and 1 more	Core, formats
conflicted	quality	Spelled `conflict`, `conflicted`, `conflicted-copy`, `mergeconflict`, `sync_conflict`	Core, negative lexicon
confusion matrix	statistic	Spelled `confusion`, `tp`, `fp`, `tn`, `fn`	Core, statistics
contaminated	quality	Spelled `contaminated`, `contamination`, `contam`, `dirty`, `infected`	Core, negative lexicon
control	condition	Spelled `ctrl`, `ctl`, `control`, `controls`, `untreated` and 2 more	Core, process
converted	stage	Spelled `conv`, `converted`, `conversion`, `transcoded`, `reformatted`	Core, process
copy	version	Spelled `copy`, `duplicate`, `dup`, `clone`	Core, time and versions
corrected	stage	Spelled `corr`, `corrected`, `correction`, `adjusted`	Core, process
correlation	statistic	Spelled `corr`, `correlation`, `pearson`, `spearman`, `kendall` and 2 more	Core, statistics
correspondence	file role	Spelled `email`, `letter`, `correspondence`, `message`, `reply`	Core, file roles
count	statistic	Spelled `n`, `count`, `counts`, `number`, `freq` and 2 more	Core, statistics
cropped	stage	Spelled `crop`, `cropped`, `cropping`, `trimmed`	Core, process
cross validation	statistic	Spelled `cv_fold`, `crossval`, `kfold`, `holdout`, `train` and 3 more	Core, statistics
cumulative distribution	file role	Spelled `cdf`, `ecdf`	Core, file roles
curie	unit	Spelled `Ci`, `curie`	Core, units
cytometer	instrument	Spelled `cytometer`, `flowcytometer`, `facs`, `sorter`, `cellsorter`	Core, instruments
dalton	unit	Spelled `Da`, `dalton`, `daltons`, `amu`	Core, units
database table file	format	Spelled `frm`, `myd`, `myi`, `opt`	Core, formats
dataset	dataset	Spelled `dataset`, `datasets`, `data`, `ds`	Core, process
day	unit	Spelled `d`, `day`, `days`, `dpi`, `dpf`	Core, units
debug	quality	Spelled `debug`, `debugging`, `dbg`, `verbose_out`, `tracefile`	Core, negative lexicon
december	date	Canonical `12`. Spelled `dec`, `december`	Core, time and versions
deconvolved	stage	Spelled `decon`, `deconv`, `deconvolved`, `deconvolution`	Core, process
default name	quality	Spelled `document1`, `document2`, `book1`, `sheet1`, `presentation1` and 3 more	Core, negative lexicon
degree	unit	Spelled `deg`, `°`, `degree`, `degrees`	Core, units
delete	quality	Spelled `delete`, `deleteme`, `delete-me`, `todelete`, `toremove` and 4 more	Core, negative lexicon
dendrogram	statistic	Spelled `dendrogram`, `linkage`, `tree_plot`	Core, statistics
denoised	stage	Spelled `denoised`, `denoise`, `denoising`, `noisereduced`	Core, process
density plot	file role	Spelled `kde`, `gkde`, `densityplot`, `density-plot`	Core, file roles
deprecated	quality	Spelled `deprecated`, `deprec`, `superseded`, `retired`, `defunct`	Core, negative lexicon
dictionary file	file role	Spelled `dictionary`, `glossary`, `codebook`, `lookup`, `mapping` and 3 more	Core, file roles
difference	statistic	Spelled `diff`, `difference`, `delta`, `change`	Core, statistics
diffusion coefficient	statistic	Spelled `deff`, `d_eff`, `diffusion_coefficient`, `diffusion-coefficient`, `diffusivity`	Core, statistics
dimensionality reduction	statistic	Spelled `tsne`, `t-sne`, `umap`, `lda`, `ica` and 3 more	Core, statistics
distance	statistic	Spelled `dist`, `distance`, `euclidean`, `cosine`, `jaccard` and 2 more	Core, statistics
do not analyse	quality	Spelled `donotanalyse`, `do-not-analyse`, `do_not_analyse`, `donotanalyze`, `do-not-analyze` and 3 more	Core, negative lexicon
do not use	quality	Spelled `donotuse`, `do-not-use`, `do_not_use`, `dontuse`, `dont-use` and 2 more	Core, negative lexicon
dots per inch	unit	Spelled `dpi`, `DPI`, `ppi`	Core, units
downsampled	stage	Spelled `downsampled`, `downsample`, `decimated`, `subsampled`	Core, process
draft	version	Spelled `draft`, `drafts`, `wip`, `work-in-progress`	Core, time and versions
dummy	quality	Spelled `dummy`, `placeholder`, `stub`, `fake`, `mock_data` and 2 more	Core, negative lexicon
duplicate	quality	Spelled `dup`, `dupe`, `duplicate`, `copy2`, `copy3` and 5 more	Core, negative lexicon
editor backup	quality	Spelled `~$`, `.swp`, `.swo`, `.bak~`, `#autosave#` and 1 more	Core, filesystem noise
electronvolt	unit	Spelled `eV`, `electronvolt`	Core, units
embedded database	format	Spelled `sqlite`, `duckdb`, `db`	Core, formats
emphatic	quality	Spelled `ACTUAL`, `REAL`, `PROPER`, `DEFINITELY`, `PLEASE` and 1 more	Core, negative lexicon
environment `environment_file`	format	Spelled `env`, `envrc`	Core, formats
error output `error_stream`	format	Spelled `err`, `stderr`	Core, formats
example	quality	Spelled `example`, `demo`, `sample_file`, `toy`, `tutorial`	Core, negative lexicon
excluded	quality	Spelled `excluded`, `exclude`, `omitted`, `dropped`, `discarded` and 3 more	Core, negative lexicon
executable `executable_format`	format	Spelled `exe`, `dll`, `dylib`, `so`, `cpl`	Core, formats
experiment	experiment	Spelled `exp`, `expt`, `experiment`, `experiments`	Core, process
exponential	statistic	Spelled `exp_fit`, `exponential`, `decay`, `growth`	Core, statistics
export	stage	Spelled `export`, `exported`, `exports`, `published`, `shared` and 2 more	Core, process
f score	statistic	Spelled `f1`, `fscore`, `f-score`, `fbeta`	Core, statistics
fahrenheit	unit	Spelled `degF`, `°F`, `fahrenheit`	Core, units
failed	quality	Spelled `failed`, `failure`, `fail`, `crashed`, `aborted` and 1 more	Core, negative lexicon
failed run	status	Spelled `error`, `errored`	Core, process
farad	unit	Spelled `F`, `farad`	Core, units
february	date	Canonical `02`. Spelled `feb`, `february`	Core, time and versions
femtogram	unit	Spelled `fg`, `femtogram`	Core, units
femtomolar	unit	Spelled `fM`, `femtomolar`	Core, units
femtomole	unit	Spelled `fmol`, `femtomole`	Core, units
figure	file role	Spelled `fig`, `figure`, `figures`, `panel`, `panels` and 2 more	Core, file roles
filter	instrument	Spelled `filter`, `filters`, `filterset`, `dichroic`, `emission_filter` and 4 more	Core, instruments
filtered	stage	Spelled `filt`, `filtered`, `filtering`	Core, process
final	version	Spelled `final`, `fin`, `finished`	Core, time and versions
final final	quality	Spelled `finalfinal`, `final_final`, `final-final`, `finalfinalfinal`, `reallyfinal` and 2 more	Core, negative lexicon
fisher exact	statistic	Spelled `fisher`, `fishers`, `fisher-exact`	Core, statistics
fit	statistic	Spelled `fit`, `fitted`, `fitting`, `model`, `modelled` and 1 more	Core, statistics
fixme	quality	Spelled `fixme`, `fix-me`, `tofix`, `needsfix`, `broken_fix` and 3 more	Core, negative lexicon
fold	unit	Spelled `x`, `X`, `fold`, `-fold`	Core, units
fold change	statistic	Spelled `fc`, `foldchange`, `fold-change`, `log2fc`, `logfc`	Core, statistics
font `font_format`	format	Spelled `ttf`, `otf`, `woff`, `woff2`	Core, formats
foot	unit	Spelled `ft`, `foot`, `feet`	Core, units
for	connective	Spelled `for`	Core, connecting words
Fortran module `fortran_module`	format	Spelled `mod`	Core, formats
frame	part	Spelled `frame`, `frames`	Core, process
frames per second	unit	Spelled `fps`, `FPS`	Core, units
freezer	instrument	Spelled `freezer`, `fridge`, `minus80`, `-80`, `-20` and 3 more	Core, instruments
friday	date	Spelled `friday`	Core, time and versions
from	connective	Spelled `from`	Core, connecting words
gaussian	statistic	Spelled `gaussian`, `normal`, `lorentzian`, `voigt`	Core, statistics
gel documentation	instrument	Spelled `geldoc`, `gel-doc`, `imager`, `licor`, `chemidoc` and 1 more	Core, instruments
gibibyte	unit	Spelled `GiB`, `gibibyte`	Core, units
gigabyte	unit	Spelled `GB`, `gigabyte`	Core, units
gigahertz	unit	Spelled `GHz`, `gigahertz`	Core, units
gigaohm	unit	Spelled `Gohm`, `GΩ`, `gigaohm`	Core, units
gram	unit	Spelled `g`, `gram`, `grams`, `gm`	Core, units
gray	unit	Spelled `Gy`, `gray`	Core, units
Groovy script `groovy_script`	format	Spelled `groovy`	Core, formats
group	condition	Spelled `group`, `groups`, `arm`, `arms`, `cohort` and 1 more	Core, process
heatmap	file role	Spelled `heatmap`, `heatmaps`, `heat-map`, `heat_map`	Core, file roles
hertz	unit	Spelled `Hz`, `hertz`	Core, units
histogram	file role	Spelled `histogram`, `histograms`, `hist`	Core, file roles
holm	statistic	Spelled `holm`, `sidak`	Core, statistics
hour	unit	Spelled `h`, `hr`, `hrs`, `hour`, `hours`	Core, units
icon `icon_format`	format	Spelled `ico`, `icns`	Core, formats
ignore	quality	Spelled `ignore`, `ignored`, `ignoreme`, `disregard`, `skipme`	Core, negative lexicon
Illustrator document `illustrator_document`	format	Spelled `ai`	Core, formats
image	file role	Spelled `image`, `images`, `img`, `picture`, `pic` and 4 more	Core, file roles
image format	format	Spelled `tif`, `tiff`, `ometiff`, `ome-tiff`, `ome.tif` and 34 more	Core, formats
ImageJ macro `imagej_macro`	format	Spelled `ijm`	Core, formats
inch	unit	Spelled `in`, `inch`, `inches`, `"`	Core, units
incubator	instrument	Spelled `incubator`, `incubation_chamber`, `co2`, `environmental_chamber`, `heated_stage`	Core, instruments
INI `ini_document`	format	Spelled `ini`	Core, formats
input data	file role	Spelled `input`, `inputs`	Core, file roles
intercept	statistic	Spelled `intercept`, `offset_term`, `b_coef`	Core, statistics
intermediate	stage	Spelled `intermediate`, `interim`, `working`, `scratch_stage`, `staging`	Core, process
interquartile range	statistic	Spelled `iqr`	Core, statistics
into	connective	Spelled `into`	Core, connecting words
invalid	quality	Spelled `invalid`, `bogus`, `nonsense`, `garbage`, `junk` and 1 more	Core, negative lexicon
inventory file	file role	Spelled `inventory`, `stock`, `registry`, `database_export`, `listing`	Core, file roles
iteration	replicate	Spelled `iter`, `iteration`, `iterations`, `epoch`	Core, time and versions
iWork document `iwork_document`	format	Spelled `iwa`, `key`, `pages`, `numbers`	Core, formats
january	date	Canonical `01`. Spelled `jan`, `january`	Core, time and versions
Java bytecode `java_bytecode`	format	Spelled `class`, `jar`	Core, formats
Java source `java_source`	format	Spelled `java`, `src`	Core, formats
JavaScript `javascript_source`	format	Spelled `js`, `mjs`, `cjs`	Core, formats
job	process	Spelled `job`, `jobs`, `task`, `tasks`	Core, process
joule	unit	Spelled `J`, `joule`, `joules`	Core, units
july	date	Canonical `07`. Spelled `jul`, `july`	Core, time and versions
june	date	Canonical `06`. Spelled `jun`, `june`	Core, time and versions
kelvin	unit	Spelled `K`, `kelvin`	Core, units
keyboard mash	quality	Spelled `asdf`, `asdfasdf`, `qwerty`, `test123`, `foo` and 2 more	Core, negative lexicon
kibibyte	unit	Spelled `KiB`, `kibibyte`	Core, units
kilobyte	unit	Spelled `KB`, `kB`, `kilobyte`	Core, units
kilocalorie	unit	Spelled `kcal`, `kilocalorie`, `Cal`	Core, units
kilodalton	unit	Spelled `kDa`, `kilodalton`	Core, units
kiloelectronvolt	unit	Spelled `keV`	Core, units
kilogram	unit	Spelled `kg`, `kilogram`, `kilograms`	Core, units
kilohertz	unit	Spelled `kHz`, `kilohertz`	Core, units
kilojoule	unit	Spelled `kJ`, `kilojoule`	Core, units
kilometre	unit	Spelled `km`, `kilometre`, `kilometer`	Core, units
kilopascal	unit	Spelled `kPa`, `kilopascal`	Core, units
kolmogorov smirnov	statistic	Spelled `ks`, `kstest`, `kolmogorov-smirnov`	Core, statistics
kruskal wallis	statistic	Spelled `kruskal`, `kruskal-wallis`	Core, statistics
kymograph	file role	Spelled `kymograph`, `kymographs`, `kymo`	Core, file roles
lamp	instrument	Spelled `lamp`, `led`, `arc`, `halogen`, `xenon` and 2 more	Core, instruments
language cache	quality	Spelled `__pycache__`, `.pyc`, `.pyo`, `.ipynb_checkpoints`, `.Rhistory` and 6 more	Core, filesystem noise
laser	instrument	Spelled `laser`, `lasers`, `laserline`, `excitation_source`	Core, instruments
latest	version	Spelled `latest`, `current`, `newest`, `head`	Core, time and versions
LaTeX source `latex_source`	format	Spelled `tex`, `latex`	Core, formats
levene	statistic	Spelled `levene`, `bartlett`	Core, statistics
licence	file role	Spelled `license`, `licence`, `copying`, `copyright`, `notice`	Core, file roles
limit of detection	statistic	Spelled `lod`, `loq`, `limit-of-detection`	Core, statistics
linear	statistic	Spelled `linear`, `lin`	Core, statistics
linux metadata	quality	Spelled `.directory`, `.Trash-1000`, `lost+found`	Core, filesystem noise
litre	unit	Spelled `L`, `l`, `litre`, `litres`, `liter` and 1 more	Core, units
lock file	format	Spelled `lck`, `lock`	Core, formats
log	process	Spelled `log`, `logs`, `logfile`, `stdout`, `stderr` and 2 more	Core, process
log file	format	Spelled `log`	Core, formats
logarithm	statistic	Spelled `log`, `ln`, `log2`, `log10`, `logged`	Core, statistics
logistic	statistic	Spelled `logistic`, `sigmoid`, `hill`, `dose-response`, `ic50` and 1 more	Core, statistics
lookup table	format	Spelled `lut`	Core, formats
lux	unit	Spelled `lx`, `lux`	Core, units
macos metadata	quality	Spelled `.DS_Store`, `._`, `__MACOSX`, `.Spotlight-V100`, `.fseventsd` and 3 more	Core, filesystem noise
magnification	unit	Spelled `x`, `X`	Core, units
manifest	process	Spelled `manifest`, `index`, `inventory`, `listing`, `catalog` and 1 more	Core, process
manipulator	instrument	Spelled `manipulator`, `micromanipulator`, `injector`, `puller`	Core, instruments
mann whitney	statistic	Spelled `mannwhitney`, `mann-whitney`, `wilcoxon`, `ranksum`, `signedrank`	Core, statistics
march	date	Canonical `03`. Spelled `mar`, `march`	Core, time and versions
markdown	format	Spelled `md`, `markdown`, `mdown`	Core, formats
marked good `good`	quality	Spelled `good`	Core, quality marks
marked unwell `looks_unwell`	quality	Spelled `sick`, `unhealthy`, `unwell`	Core, quality marks
markup `markup_document`	format	Spelled `html`, `htm`, `xhtml`	Core, formats
masked	stage	Spelled `mask`, `masks`, `masked`, `masking`	Core, process
mass spectrometer	instrument	Spelled `massspec`, `mass-spec`, `spectrometer`, `ms_instrument`	Core, instruments
MATLAB source `matlab_source`	format	Spelled `m`	Core, formats
maximum	statistic	Spelled `max`, `maximum`, `highest`, `peak`	Core, statistics
may	date	Canonical `05`. Spelled `may`	Core, time and versions
mean	statistic	Spelled `mean`, `avg`, `ave`, `average`, `mu`	Core, statistics
mebibyte	unit	Spelled `MiB`, `mebibyte`	Core, units
median	statistic	Spelled `median`, `med`, `p50`	Core, statistics
megabyte	unit	Spelled `MB`, `megabyte`	Core, units
megadalton	unit	Spelled `MDa`, `megadalton`	Core, units
megaelectronvolt	unit	Spelled `MeV`	Core, units
megahertz	unit	Spelled `MHz`, `megahertz`	Core, units
megaohm	unit	Spelled `Mohm`, `MΩ`, `megaohm`	Core, units
megapascal	unit	Spelled `MPa`, `megapascal`	Core, units
merged	stage	Spelled `merge`, `merged`, `combined`, `joined`, `concatenated` and 1 more	Core, process
metadata	file role	Spelled `metadata`, `meta`, `header`, `headers`, `sidecar` and 2 more	Core, file roles
metre	unit	Spelled `m`, `metre`, `metres`, `meter`, `meters`	Core, units
microampere	unit	Spelled `uA`, `µA`, `μA`, `microamp`	Core, units
microgram	unit	Spelled `ug`, `µg`, `μg`, `mcg`, `microgram` and 1 more	Core, units
microgram per microlitre	unit	Spelled `ug/uL`, `µg/µL`, `ugul`	Core, units
microgram per millilitre	unit	Spelled `ug/mL`, `µg/mL`, `μg/mL`, `ugml`, `ugperml`	Core, units
microlitre	unit	Spelled `uL`, `ul`, `µL`, `µl`, `μL` and 2 more	Core, units
micrometre	unit	Spelled `um`, `µm`, `μm`, `micron`, `microns` and 2 more	Core, units
micromolar	unit	Spelled `uM`, `µM`, `μM`, `micromolar`, `umol/L`	Core, units
micromole	unit	Spelled `umol`, `µmol`, `μmol`, `micromole`	Core, units
microscope	instrument	Spelled `microscope`, `scope`, `micro`, `imaging_system`	Core, instruments
microsecond	unit	Spelled `us`, `µs`, `μs`, `usec`, `microsecond`	Core, units
microvolt	unit	Spelled `uV`, `µV`, `μV`, `microvolt`	Core, units
microwatt	unit	Spelled `uW`, `µW`, `μW`, `microwatt`	Core, units
milliampere	unit	Spelled `mA`, `milliamp`	Core, units
millibar	unit	Spelled `mbar`, `millibar`	Core, units
milligram	unit	Spelled `mg`, `milligram`, `milligrams`	Core, units
milligram per millilitre	unit	Spelled `mg/mL`, `mg/ml`, `mgml`, `mgpermL`	Core, units
millilitre	unit	Spelled `mL`, `ml`, `millilitre`, `milliliter`, `cc`	Core, units
millimetre	unit	Spelled `mm`, `millimetre`, `millimeter`	Core, units
millimolar	unit	Spelled `mM`, `millimolar`, `mmol/L`	Core, units
millimole	unit	Spelled `mmol`, `millimole`	Core, units
millisecond	unit	Spelled `ms`, `msec`, `millisecond`, `milliseconds`	Core, units
millivolt	unit	Spelled `mV`, `millivolt`	Core, units
milliwatt	unit	Spelled `mW`, `milliwatt`	Core, units
minimum	statistic	Spelled `min`, `minimum`, `lowest`	Core, statistics
minute	unit	Spelled `min`, `mins`, `minute`, `minutes`	Core, units
mode	statistic	Spelled `mode`	Core, statistics
molar	unit	Spelled `M`, `molar`, `mol/L`, `mol/l`	Core, units
mole	unit	Spelled `mol`, `mole`, `moles`	Core, units
monday	date	Spelled `monday`	Core, time and versions
month	unit	Spelled `mo`, `month`, `months`	Core, units
morning	date	Spelled `am`, `morning`	Core, time and versions
movie	file role	Spelled `movie`, `movies`, `video`, `videos`, `clip` and 1 more	Core, file roles
nanoampere	unit	Spelled `nA`, `nanoamp`	Core, units
nanogram	unit	Spelled `ng`, `nanogram`, `nanograms`	Core, units
nanogram per millilitre	unit	Spelled `ng/mL`, `ng/ml`, `ngml`, `ngperml`	Core, units
nanolitre	unit	Spelled `nL`, `nl`, `nanolitre`, `nanoliter`	Core, units
nanometre	unit	Spelled `nm`, `nanometre`, `nanometer`	Core, units
nanomolar	unit	Spelled `nM`, `nanomolar`, `nmol/L`	Core, units
nanomole	unit	Spelled `nmol`, `nanomole`	Core, units
nanosecond	unit	Spelled `ns`, `nsec`, `nanosecond`	Core, units
nanosiemens	unit	Spelled `nS`, `nanosiemens`	Core, units
new folder	quality	Spelled `newfolder`, `new folder`, `new-folder`, `untitledfolder`, `folder1` and 1 more	Core, negative lexicon
noise	statistic	Spelled `noise`, `background`, `bg`, `blank`, `dark`	Core, statistics
nonlinear	statistic	Spelled `nonlinear`, `non-linear`, `nls`	Core, statistics
normalised	stage	Spelled `norm`, `normalised`, `normalized`, `normalisation`, `normalization`	Core, process
notebook	process	Spelled `notebook`, `notebooks`, `nb`	Core, process
notebook `notebook_format`	format	Spelled `ipynb`	Core, formats
notes	file role	Spelled `notes`, `note`, `memo`, `comments`, `remarks` and 4 more	Core, file roles
november	date	Canonical `11`. Spelled `nov`, `november`	Core, time and versions
numerical aperture	unit	Spelled `NA`	Core, units
objective	instrument	Spelled `objective`, `obj`, `lens`, `lenses`	Core, instruments
obsolete	quality	Spelled `obsolete`, `outdated`, `stale`, `expired`, `legacy` and 1 more	Core, negative lexicon
october	date	Canonical `10`. Spelled `oct`, `october`	Core, time and versions
of	connective	Spelled `of`	Core, connecting words
ohm	unit	Spelled `ohm`, `ohms`, `Ω`	Core, units
or	connective	Spelled `or`	Core, connecting words
original	version	Spelled `original`, `source`, `master`	Core, time and versions
original kept aside `kept_original`	version	Spelled `orig`	Core, time and versions
overnight	date	Spelled `overnight`, `o/n`, `ovn`	Core, time and versions
p value	statistic	Spelled `p`, `pval`, `pvalue`, `p-value`, `pvals`	Core, statistics
package relationship part	format	Spelled `rels`	Core, formats
partial	status	Spelled `partial`, `incomplete`, `truncated`, `unfinished`	Core, process
parts per billion	unit	Spelled `ppb`	Core, units
parts per million	unit	Spelled `ppm`	Core, units
pascal	unit	Spelled `Pa`, `pascal`	Core, units
PDF `portable_document`	format	Spelled `pdf`	Core, formats
pending	status	Spelled `pending`, `queued`, `waiting`, `todo`, `scheduled`	Core, process
per	connective	Spelled `per`	Core, connecting words
percent	unit	Spelled `%`, `pct`, `percent`	Core, units
percent change	statistic	Spelled `pctchange`, `percent-change`, `relchange`	Core, statistics
percent volume volume	unit	Spelled `%v/v`, `vv`, `v/v`	Core, units
percent weight volume	unit	Spelled `%w/v`, `wv`, `w/v`	Core, units
percentile	statistic	Spelled `pct`, `percentile`, `quantile`, `p95`, `p99`	Core, statistics
Perl `perl_source`	format	Spelled `pl`, `pm`	Core, formats
petabyte	unit	Spelled `PB`, `petabyte`	Core, units
ph meter	instrument	Spelled `phmeter`, `ph-meter`, `probe_ph`	Core, instruments
picoampere	unit	Spelled `pA`, `picoamp`	Core, units
picofarad	unit	Spelled `pF`, `picofarad`	Core, units
picogram	unit	Spelled `pg`, `picogram`, `picograms`	Core, units
picolitre	unit	Spelled `pL`, `pl`, `picolitre`, `picoliter`	Core, units
picometre	unit	Spelled `pm`, `picometre`, `picometer`	Core, units
picomolar	unit	Spelled `pM`, `picomolar`, `pmol/L`	Core, units
picomole	unit	Spelled `pmol`, `picomole`	Core, units
pipeline	process	Spelled `pipeline`, `workflow`, `flow`, `dag`	Core, process
pixel	unit	Spelled `px`, `pixel`, `pixels`	Core, units
plain text	format	Spelled `txt`, `text`	Core, formats
plate	vessel	Spelled `plate`, `plates`, `wellplate`, `microplate`	Core, process
plate reader	instrument	Spelled `platereader`, `plate-reader`, `reader`, `spectrophotometer`, `luminometer` and 2 more	Core, instruments
playlist `playlist_format`	format	Spelled `m3u`, `m3u8`, `pls`	Core, formats
plot	file role	Spelled `plot`, `plots`, `chart`, `charts`, `graph` and 2 more	Core, file roles
polynomial	statistic	Spelled `poly`, `polynomial`, `quadratic`, `cubic`	Core, statistics
pooled	stage	Spelled `pooled`, `pooling`, `metaanalysis`, `meta-analysis`, `meta_analysis` and 4 more	Core, process
position	position	Spelled `pos`, `position`, `positions`, `site`, `sites` and 2 more	Core, process
pre-treatment `pretreatment`	condition	Spelled `pre`, `pretreatment`, `pre-treatment`, `pretreated`, `pre-treated`	Core, process
precision	statistic	Spelled `precision`, `ppv`	Core, statistics
preprocessed	stage	Spelled `prep`, `prepped`, `preprocessed`, `preprocessing`, `pre-processed`	Core, process
presentation	file role	Spelled `presentation`, `slides`, `deck`, `talk`, `seminar` and 1 more	Core, file roles
presentation `slide_deck_format`	format	Spelled `pptx`, `ppt`, `odp`	Core, formats
previous	version	Spelled `prev`, `previous`, `prior`, `last`	Core, time and versions
principal component analysis	statistic	Spelled `pca`, `pc1`, `pc2`, `principal`	Core, statistics
processed	stage	Spelled `processed`, `processing`, `proc`	Core, process
program output	format	Spelled `out`	Core, formats
project	project	Spelled `project`, `proj`, `programme`, `program`	Core, process
projected	stage	Spelled `proj`, `projected`, `projection`	Core, process
protocol	file role	Spelled `protocol`, `protocols`, `sop`, `procedure`, `method` and 3 more	Core, file roles
psi	unit	Spelled `psi`	Core, units
Python bytecode `python_bytecode`	format	Spelled `pyc`, `pyo`	Core, formats
Python source `python_source`	format	Spelled `py`, `pyi`, `pyx`	Core, formats
quantification	stage	Spelled `quant`, `quantified`, `quantification`, `measurements`, `measured`	Core, process
quarantine	quality	Spelled `quarantine`, `quarantined`, `isolated`, `held`, `onhold` and 2 more	Core, negative lexicon
quartile	statistic	Spelled `q1`, `q3`, `quartile`, `quartiles`	Core, statistics
questionable	quality	Spelled `questionable`, `suspect`, `suspicious`, `dodgy`, `sketchy` and 3 more	Core, negative lexicon
R Markdown `r_markdown`	format	Spelled `rmd`, `rmarkdown`	Core, formats
R source `r_source`	format	Spelled `r`	Core, formats
r squared	statistic	Spelled `r2`, `rsq`, `rsquared`, `r-squared`, `adjr2`	Core, statistics
R workspace `r_workspace`	format	Spelled `rds`, `rdata`	Core, formats
radian	unit	Spelled `rad`, `radian`, `radians`	Core, units
range	statistic	Spelled `range`, `spread`	Core, statistics
ratio	statistic	Spelled `ratio`, `quotient`, `relative`	Core, statistics
raw	stage	Spelled `raw`, `unprocessed`, `untouched`, `asacquired`, `as-acquired` and 3 more	Core, process
readme	file role	Spelled `readme`, `read-me`, `aboutthis`, `about`	Core, file roles
receiver operating characteristic	statistic	Spelled `roc`, `auroc`	Core, statistics
recovered	quality	Spelled `recovered`, `recovery`, `restored`, `salvaged`, `autosave` and 2 more	Core, negative lexicon
redo	quality	Spelled `redo`, `redone`, `rerun_after_fail`, `repeat_of`, `attempt2` and 3 more	Core, negative lexicon
reference data	file role	Spelled `reference`, `ref`, `standard`, `standards`, `groundtruth` and 4 more	Core, file roles
reference manager library `reference_library`	format	Spelled `enl`	Core, formats
regression	statistic	Spelled `reg`, `regression`, `lm`, `glm`, `ols` and 3 more	Core, statistics
relative centrifugal force	unit	Spelled `rcf`, `xg`, `x g`, `RCF`	Core, units
release	version	Spelled `rel`, `release`	Core, time and versions
replicate	replicate	Spelled `rep`, `reps`, `replicate`, `replicates`, `repeat`	Core, time and versions
report	stage	Spelled `report`, `reports`, `writeup`, `write-up`, `manuscript` and 4 more	Core, process
rerun	replicate	Spelled `rerun`, `redo`, `again`, `retry`	Core, time and versions
residual	statistic	Spelled `resid`, `residual`, `residuals`, `error_term`	Core, statistics
resized	stage	Spelled `resize`, `resized`, `rescaled`, `scaled`	Core, process
reStructuredText `restructured_text`	format	Spelled `rst`	Core, formats
revision	version	Spelled `r`, `rev`, `revision`	Core, time and versions
revolutions per minute	unit	Spelled `rpm`, `RPM`	Core, units
round	replicate	Spelled `round`, `rounds`, `pass`, `passes`, `cycle` and 1 more	Core, time and versions
Ruby source `ruby_source`	format	Spelled `rb`	Core, formats
run	process	Spelled `run`, `runs`, `execution`, `exec`	Core, process
running	status	Spelled `running`, `active`, `inprogress`, `in-progress`	Core, process
sample	sample	Spelled `sample`, `samples`, `spec`, `specimen`, `specimens`	Core, process
saturday	date	Spelled `saturday`	Core, time and versions
scanner	instrument	Spelled `scanner`, `slidescanner`, `gel_scanner`, `densitometer`	Core, instruments
scatter plot	file role	Spelled `scatter`, `scatterplot`, `scatter-plot`	Core, file roles
schema	file role	Spelled `schema`, `schemas`, `spec`, `specification`, `definition` and 1 more	Core, file roles
scratch	quality	Spelled `scratch`, `scratchpad`, `sandbox`, `playground`, `workspace_tmp`	Core, negative lexicon
script	process	Spelled `script`, `scripts`, `macro`, `macros`, `code`	Core, process
second	unit	Spelled `s`, `sec`, `secs`, `second`, `seconds`	Core, units
segment	part	Spelled `segment`, `segments`	Core, process
segmented	stage	Spelled `seg`, `segmented`, `segmentation`	Core, process
sensitivity	statistic	Spelled `sensitivity`, `recall`, `tpr`	Core, statistics
september	date	Canonical `09`. Spelled `sep`, `sept`, `september`	Core, time and versions
sequencer	instrument	Spelled `sequencer`, `sequencing_machine`, `flowcell_machine`	Core, instruments
session	session	Spelled `session`, `sessions`, `sitting`	Core, process
shapiro wilk	statistic	Spelled `shapiro`, `shapiro-wilk`	Core, statistics
shell script	format	Spelled `sh`, `bash`, `zsh`	Core, formats
siemens	unit	Spelled `S`, `siemens`	Core, units
sievert	unit	Spelled `Sv`, `sievert`	Core, units
signal	statistic	Spelled `signal`, `sig_intensity`, `amplitude`	Core, statistics
signal to noise	statistic	Spelled `snr`, `s/n`, `sbr`, `cnr`	Core, statistics
significance	statistic	Spelled `sig`, `significant`, `ns`, `nonsignificant`, `alpha`	Core, statistics
single	quantifier	Spelled `single`	Core, process
skipped	status	Spelled `skipped`, `skip`, `bypassed`, `excluded`	Core, process
slide	vessel	Spelled `slide`, `slides`, `coverslip`, `chamber`, `dish` and 3 more	Core, process
slope	statistic	Spelled `slope`, `gradient`, `m_coef`	Core, statistics
smoothed	stage	Spelled `smooth`, `smoothed`, `smoothing`	Core, process
specificity	statistic	Spelled `specificity`, `tnr`	Core, statistics
SQL `sql_source`	format	Spelled `sql`	Core, formats
stage	instrument	Spelled `stage`, `xystage`, `zstage`, `piezo`, `motorised` and 1 more	Core, instruments
standard deviation	statistic	Spelled `sd`, `std`, `stdev`, `stddev`, `sigma`	Core, statistics
standard error	statistic	Spelled `se`, `sem`, `stderr`	Core, statistics
stated replicate count	count	Spelled `n`	Core, time and versions
step size	statistic	Spelled `step_size`, `step_sizes`, `step-size`, `step-sizes`	Core, statistics
stitched	stage	Spelled `stitch`, `stitched`, `stitching`, `mosaic`	Core, process
structured format	format	Spelled `json`, `yaml_format`, `toml_format`, `xml_format`, `ini_format` and 1 more	Core, formats
study	experiment	Spelled `study`, `studies`, `investigation`	Core, process
subject	subject	Spelled `subject`, `subjects`, `animal`, `animals`, `donor` and 1 more	Core, process
subset	stage	Spelled `subset`, `selection`, `selected`, `filtered_subset`	Core, process
sum	statistic	Spelled `sum`, `total`, `integral`, `integrated`, `auc_area`	Core, statistics
summary	stage	Spelled `summary`, `summaries`, `summarised`, `summarized`, `aggregate` and 2 more	Core, process
sunday	date	Spelled `sunday`	Core, time and versions
superseded by	quality	Spelled `replacedby`, `replaced-by`, `supersededby`, `seeinstead`	Core, negative lexicon
supplementary	file role	Spelled `supp`, `suppl`, `supplementary`, `supplement`, `si` and 2 more	Core, file roles
sync artifact	quality	Spelled `.dropbox`, `.dropbox.cache`, `.onedrive`, `Icon?`, `conflicted copy` and 1 more	Core, filesystem noise
t test	statistic	Spelled `ttest`, `t-test`, `students`, `welch`, `paired_t`	Core, statistics
table	file role	Spelled `table`, `tables`, `tab`, `sheet`, `worksheet` and 1 more	Core, file roles
tabular format	format	Spelled `csv`, `tsv`, `parquet`, `feather`, `arrow` and 3 more	Core, formats
tebibyte	unit	Spelled `TiB`, `tebibyte`	Core, units
technical replicate	replicate	Spelled `tech`, `technical`, `techrep`, `tr`	Core, time and versions
template	file role	Spelled `template`, `templates`, `boilerplate`, `blank_form`	Core, file roles
temporary	quality	Spelled `tmp`, `temp`, `temporary`, `transient`, `ephemeral`	Core, negative lexicon
temporary file	format	Spelled `tmp`	Core, formats
terabyte	unit	Spelled `TB`, `terabyte`	Core, units
test artifact	quality	Spelled `testfile`, `test-file`, `trialrun`, `dryrun`, `dry-run` and 1 more	Core, negative lexicon
text clipping	format	Spelled `textclipping`	Core, formats
than	connective	Spelled `than`	Core, connecting words
the	connective	Spelled `the`	Core, connecting words
thermocycler	instrument	Spelled `thermocycler`, `pcrmachine`, `pcr-machine`, `cycler`, `lightcycler` and 1 more	Core, instruments
threshold	statistic	Spelled `threshold`, `cutoff`, `cut-off`, `gate`, `gating` and 1 more	Core, statistics
thresholded	stage	Spelled `thresh`, `threshold`, `thresholded`, `binarised`, `binarized`	Core, process
thumbnail	file role	Spelled `thumb`, `thumbnail`, `thumbnails`, `preview`, `icon` and 1 more	Core, file roles
thursday	date	Spelled `thursday`	Core, time and versions
time lag	statistic	Spelled `tlag`, `t_lag`, `time_lag`, `lag_time`, `timelag`	Core, statistics
timepoint	timepoint	Spelled `tp`, `timepoint`, `timepoints`, `time-point`, `timecourse` and 1 more	Core, process
to	connective	Spelled `to`	Core, connecting words
today	date	Spelled `today`	Core, time and versions
todo	quality	Spelled `todo`, `to-do`, `pending_work`, `unfinished`, `incomplete` and 2 more	Core, negative lexicon
TOML `toml_document`	format	Spelled `toml`	Core, formats
torr	unit	Spelled `Torr`, `torr`, `mmHg`	Core, units
treatment	condition	Spelled `treat`, `treated`, `treatment`, `treatments`, `dosed`	Core, process
trial	replicate	Spelled `trial`, `trials`, `attempt`, `attempts`, `take` and 1 more	Core, time and versions
tris carboxyethyl phosphine	reagent	Spelled `tcep`	Core, reagents
tuesday	date	Spelled `tuesday`	Core, time and versions
tukey	statistic	Spelled `tukey`, `hsd`, `dunnett`, `scheffe`	Core, statistics
turning angle	statistic	Spelled `cos_theta`, `costheta`, `turning_angle`, `turning-angle`	Core, statistics
unaffiliated	stage	Spelled `misc`, `miscellaneous`, `other`, `unsorted`, `unfiled` and 2 more	Core, process
unsure	quality	Spelled `unsure`, `uncertain`, `maybe`, `perhaps`, `possibly` and 6 more	Core, negative lexicon
untitled	quality	Spelled `untitled`, `unnamed`, `noname`, `no-name`, `nameless`	Core, negative lexicon
upsampled	stage	Spelled `upsampled`, `upsample`, `interpolated`	Core, process
use this one	quality	Spelled `usethis`, `use-this`, `usethisone`, `thisone`, `correctone` and 2 more	Core, negative lexicon
variance	statistic	Spelled `var`, `variance`	Core, statistics
vehicle	condition	Spelled `veh`, `vehicle`, `dmso_control`, `carrier`	Core, process
version	version	Spelled `v`, `ver`, `vers`, `version`	Core, time and versions
version control	quality	Spelled `.git`, `.svn`, `.hg`, `.gitignore`, `.gitattributes` and 1 more	Core, filesystem noise
version soup	quality	Spelled `v2final`, `v3final`, `finalv2`, `final2`, `final3` and 3 more	Core, negative lexicon
versus	connective	Spelled `vs`, `versus`	Core, connecting words
via	connective	Spelled `via`	Core, connecting words
video format	format	Spelled `avi`, `mp4`, `mov`, `mkv`, `webm` and 1 more	Core, formats
violin plot	file role	Spelled `violin`, `violins`, `violinplot`, `violin-plot`	Core, file roles
volcano plot	file role	Spelled `volcano`, `volcanoplot`, `volcano-plot`	Core, file roles
volt	unit	Spelled `V`, `volt`, `volts`	Core, units
voxel	unit	Spelled `voxel`, `voxels`	Core, units
VTK data `vtk_data`	format	Spelled `vtk`	Core, formats
watt	unit	Spelled `W`, `watt`, `watts`	Core, units
web shortcut	format	Spelled `webloc`	Core, formats
wednesday	date	Spelled `wednesday`	Core, time and versions
week	unit	Spelled `wk`, `week`, `weeks`	Core, units
well	vessel	Spelled `well`, `wells`	Core, process
wheel `python_wheel`	format	Spelled `whl`	Core, formats
wild type	condition	Spelled `wildtype`, `wild-type`, `wt`	Core, process
windows metadata	quality	Spelled `Thumbs.db`, `desktop.ini`, `ehthumbs.db`, `$RECYCLE.BIN`, `System Volume Information`	Core, filesystem noise
with	connective	Spelled `with`	Core, connecting words
without	connective	Spelled `without`	Core, connecting words
word processor document `rich_document`	format	Spelled `docx`, `doc`, `odt`, `rtf`	Core, formats
workstation	instrument	Spelled `workstation`, `desktop_machine`, `laptop`, `server`, `node` and 3 more	Core, instruments
wrong	quality	Spelled `wrong`, `incorrect`, `mistake`, `mistaken`, `oops` and 1 more	Core, negative lexicon
XML `xml_document`	format	Spelled `xml`, `xsd`, `xsl`	Core, formats
YAML `yaml_document`	format	Spelled `yaml`, `yml`	Core, formats
year	unit	Spelled `y`, `yr`, `year`, `years`	Core, units
yesterday	date	Spelled `yesterday`	Core, time and versions
zscore	statistic	Spelled `z`, `zscore`, `z-score`, `standardised`, `standardized`	Core, statistics

Dictionary word

3D mesh

mesh_format · Core, formats

Kind: format
Spelled: stl, obj, ply

As YAML for a pack file

  - {term: mesh_format, canonical: "3D mesh", theme_kind: format, surfaces: [stl, obj, ply],
     extension_only: [obj, stl, ply]}

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Dictionary word

aborted

aborted · Core, process

Kind: status
Spelled: aborted, cancelled, canceled, stopped, killed, interrupted

As YAML for a pack file

  - {term: aborted, theme_kind: status, surfaces: [aborted, cancelled, canceled, stopped, killed,
     interrupted]}

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Dictionary word

accuracy

accuracy · Core, statistics

Kind: statistic
Spelled: accuracy, acc

As YAML for a pack file

  - {term: accuracy, theme_kind: statistic, surfaces: [accuracy, acc]}

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Dictionary word

acquisition

acquisition · Core, process

Kind: stage
Spelled: acq, acquisition, acquired, capture, captured, recording, recorded

As YAML for a pack file

  - {term: acquisition, theme_kind: stage, surfaces: [acq, acquisition, acquired, capture,
     captured, recording, recorded]}

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Dictionary word

adenosine diphosphate

adenosine_diphosphate · Core, reagents

Kind: reagent
Spelled: adp

As YAML for a pack file

  - {term: adenosine_diphosphate, theme_kind: reagent, surfaces: [adp]}

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Dictionary word

adenosine triphosphate

adenosine_triphosphate · Core, reagents

Kind: reagent
Spelled: atp

As YAML for a pack file

  - {term: adenosine_triphosphate, theme_kind: reagent, surfaces: [atp]}

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Dictionary word

adjusted p value

adjusted_p_value · Core, statistics

Kind: statistic
Spelled: padj, qval, qvalue, fdr, adjusted, corrected_p

As YAML for a pack file

  - {term: adjusted_p_value, theme_kind: statistic, surfaces: [padj, qval, qvalue, fdr, adjusted,
     corrected_p]}

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Dictionary word

administrative

administrative · Core, file roles

Kind: file role
Spelled: invoice, receipt, order, quote, budget, grant, approval, form and 1 more

As YAML for a pack file

  - {term: administrative, theme_kind: file_role, surfaces: [invoice, receipt, order, quote,
     budget, grant, approval, form, contract]}

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Dictionary word

Affinity document

affinity_document · Core, formats

Kind: format
Spelled: afdesign, afphoto

As YAML for a pack file

  - {term: affinity_document, canonical: "Affinity document", theme_kind: format,
     surfaces: [afdesign, afphoto], product: true}

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Dictionary word

afternoon

afternoon · Core, time and versions

Kind: date
Spelled: pm, afternoon

As YAML for a pack file

  - {term: afternoon, theme_kind: date, surfaces: [pm, afternoon]}

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Dictionary word

aligned

aligned · Core, process

Kind: stage
Spelled: aligned, alignment, registered, registration, coregistered

As YAML for a pack file

  - {term: aligned, theme_kind: stage, surfaces: [aligned, alignment, registered, registration,
     coregistered]}

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Dictionary word

ampere

ampere · Core, units

Kind: unit
Spelled: A, amp, ampere, amps

As YAML for a pack file

  - {term: ampere, theme_kind: unit, surfaces: [A, amp, ampere, amps], dimension: current,
     base: ampere, factor: 1.0, ucum: A}

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Dictionary word

amplifier

amplifier · Core, instruments

Kind: instrument
Spelled: amplifier, amp_rig, headstage, digitizer, daq, adc

As YAML for a pack file

  - {term: amplifier, theme_kind: instrument, surfaces: [amplifier, amp_rig, headstage,
     digitizer, daq, adc]}

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Dictionary word

an

an · Core, connecting words

Kind: connective
Spelled: an

As YAML for a pack file

  - {term: an, theme_kind: connective, surfaces: [an]}

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Dictionary word

analysis

analysis · Core, process

Kind: stage
Spelled: analysis, analyses, analysed, analyzed, analytic, track, tracked, tracking and 9 more

As YAML for a pack file

  - {term: analysis, theme_kind: stage, surfaces: [analysis, analyses, analysed, analyzed,
     analytic, track, tracked, tracking, tracks, trajectories, output, outputs, out, result, results,
     res, derived]}

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Dictionary word

analysis of variance

analysis_of_variance · Core, statistics

Kind: statistic
Spelled: anova, manova, ancova, two-way, one-way

As YAML for a pack file

  - {term: analysis_of_variance, theme_kind: statistic, surfaces: [anova, manova, ancova,
     "two-way", "one-way"]}

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Dictionary word

and

and · Core, connecting words

Kind: connective
Spelled: and

As YAML for a pack file

  - {term: and, theme_kind: connective, surfaces: [and]}

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Dictionary word

angstrom

angstrom · Core, units

Kind: unit
Spelled: Å, angstrom, angstroms

As YAML for a pack file

  - {term: angstrom, theme_kind: unit, surfaces: ["Å", angstrom, angstroms], dimension: length,
     base: metre, factor: 1.0e-10, ucum: Ao}

Section page ›

Dictionary word

annotated

annotated · Core, process

Kind: stage
Spelled: annotated, annotation, labelled, labeled, curated

As YAML for a pack file

  - {term: annotated, theme_kind: stage, surfaces: [annotated, annotation, labelled, labeled,
     curated]}

Section page ›

Dictionary word

annotation

annotation · Core, file roles

Kind: file role
Spelled: annotation, annotations, label, labels, roi, rois, mask_file, segmentation_file

As YAML for a pack file

  - {term: annotation, theme_kind: file_role, surfaces: [annotation, annotations, label, labels,
     roi, rois, mask_file, segmentation_file]}

Section page ›

Dictionary word

april

april · Core, time and versions

Kind: date
Canonical: 04
Spelled: apr, april

As YAML for a pack file

  - {term: april, canonical: "04", theme_kind: date, surfaces: [apr, april]}

Section page ›

Dictionary word

archive

archive_format · Core, formats

Kind: format
Spelled: zip, tar, 7z, rar

As YAML for a pack file

  - {term: archive_format, canonical: archive, theme_kind: format, surfaces: [zip, tar, "7z",
     rar]}

Section page ›

Dictionary word

archive helper

archive_helper · Core, filesystem noise

Kind: quality
Spelled: .part, .crdownload, .download, .partial, .tmp.download

As YAML for a pack file

  - {term: archive_helper, theme_kind: quality, surfaces: [".part", ".crdownload", ".download",
     ".partial", ".tmp.download"], strength: strong}

Section page ›

Dictionary word

archive only

archive_only · Core, negative lexicon

Kind: quality
Spelled: donotedit, readonly, frozen, locked, sealed

As YAML for a pack file

  - {term: archive_only, theme_kind: quality, surfaces: [donotedit, readonly, frozen, locked,
     sealed], strength: moderate}

Section page ›

Dictionary word

area under curve

area_under_curve · Core, statistics

Kind: statistic
Spelled: auc, aupr, auprc

As YAML for a pack file

  - {term: area_under_curve, theme_kind: statistic, surfaces: [auc, aupr, auprc]}

Section page ›

Dictionary word

at

at · Core, connecting words

Kind: connective
Spelled: at

As YAML for a pack file

  - {term: at, theme_kind: connective, surfaces: [at]}

Section page ›

Dictionary word

atmosphere

atmosphere · Core, units

Kind: unit
Spelled: atm, atmosphere

As YAML for a pack file

  - {term: atmosphere, theme_kind: unit, surfaces: [atm, atmosphere], dimension: pressure,
     base: pascal, factor: 101325.0, ucum: atm}

Section page ›

Dictionary word

audio

audio_format · Core, formats

Kind: format
Spelled: m4a, mp3, wav, flac, aac, aiff

As YAML for a pack file

  - {term: audio_format, canonical: audio, theme_kind: format, surfaces: [m4a, mp3, wav, flac,
     aac, aiff]}

Section page ›

Dictionary word

august

august · Core, time and versions

Kind: date
Canonical: 08
Spelled: aug, august

As YAML for a pack file

  - {term: august, canonical: "08", theme_kind: date, surfaces: [aug, august]}

Section page ›

Dictionary word

backup

backup · Core, time and versions

Kind: version
Spelled: backup, bak, bkp, bkup, back-up, archive_copy, old

As YAML for a pack file

  - {term: backup, theme_kind: version, surfaces: [backup, bak, bkp, bkup, "back-up",
     archive_copy, old]}

Section page ›

Dictionary word

bad

bad · Core, negative lexicon

Kind: quality
Spelled: bad, poor, terrible, awful, useless, rubbish

As YAML for a pack file

  - {term: bad, theme_kind: quality, surfaces: [bad, poor, terrible, awful, useless, rubbish],
     strength: strong}

Section page ›

Dictionary word

balance

balance · Core, instruments

Kind: instrument
Spelled: balance, scale_instrument, weighing

As YAML for a pack file

  - {term: balance, theme_kind: instrument, surfaces: [balance, scale_instrument, weighing]}

Section page ›

Dictionary word

bar

bar · Core, units

Kind: unit
Spelled: bar

As YAML for a pack file

  - {term: bar, theme_kind: unit, surfaces: [bar], dimension: pressure, base: pascal,
     factor: 100000.0, ucum: bar}

Section page ›

Dictionary word

baseline

baseline · Core, process

Kind: condition
Spelled: baseline, t0, timezero

As YAML for a pack file

  - {term: baseline, theme_kind: condition, surfaces: [baseline, t0, timezero]}

Section page ›

Dictionary word

batch

batch · Core, process

Kind: process
Spelled: batch, batches, bulk

As YAML for a pack file

  - {term: batch, theme_kind: process, surfaces: [batch, batches, bulk]}

Section page ›

Dictionary word

BeanShell script

beanshell_script · Core, formats

Kind: format
Spelled: bsh

As YAML for a pack file

  - {term: beanshell_script, canonical: "BeanShell script", theme_kind: format, surfaces: [bsh],
     program: true}

Section page ›

Dictionary word

becquerel

becquerel · Core, units

Kind: unit
Spelled: Bq, becquerel

As YAML for a pack file

  - {term: becquerel, theme_kind: unit, surfaces: [Bq, becquerel], dimension: radioactivity,
     base: becquerel, factor: 1.0, ucum: Bq}

Section page ›

Dictionary word

benjamini hochberg

benjamini_hochberg · Core, statistics

Kind: statistic
Spelled: bh, benjamini-hochberg

As YAML for a pack file

  - {term: benjamini_hochberg, theme_kind: statistic, surfaces: [bh, "benjamini-hochberg"]}

Section page ›

Dictionary word

binary data

generic_binary · Core, formats

Kind: format
Spelled: dat, raw, bin

As YAML for a pack file

  - {term: generic_binary, canonical: "binary data", theme_kind: format, surfaces: [dat, raw,
     bin], extension_only: [bin, raw]}

Section page ›

Dictionary word

binned

binned · Core, process

Kind: stage
Spelled: bin, binned, binning

As YAML for a pack file

  - {term: binned, theme_kind: stage, surfaces: [bin, binned, binning]}

Section page ›

Dictionary word

biological replicate

biological_replicate · Core, time and versions

Kind: replicate
Spelled: bio, biological, biorep, br

As YAML for a pack file

  - {term: biological_replicate, theme_kind: replicate, surfaces: [bio, biological, biorep, br]}

Section page ›

Dictionary word

bit

bit · Core, units

Kind: unit
Spelled: bit, bits

As YAML for a pack file

  - {term: bit, theme_kind: unit, surfaces: [bit, bits], dimension: digital_size, base: byte,
     factor: 0.125, ucum: bit}

Section page ›

Dictionary word

bonferroni

bonferroni · Core, statistics

Kind: statistic
Spelled: bonferroni, bonf

As YAML for a pack file

  - {term: bonferroni, theme_kind: statistic, surfaces: [bonferroni, bonf]}

Section page ›

Dictionary word

boxplot

boxplot · Core, file roles

Kind: file role
Spelled: boxplot, boxplots, box-plot, box_plot, box-and-whisker

As YAML for a pack file

  - {term: boxplot, theme_kind: file_role, surfaces: [boxplot, boxplots, "box-plot", box_plot,
     "box-and-whisker"], product: true}

Section page ›

Dictionary word

broken

broken · Core, negative lexicon

Kind: quality
Spelled: broken, broke, busted, corrupt, corrupted, damaged, malformed

As YAML for a pack file

  - {term: broken, theme_kind: quality, surfaces: [broken, broke, busted, corrupt, corrupted,
     damaged, malformed], strength: strong}

Section page ›

Dictionary word

build

build · Core, time and versions

Kind: version
Spelled: b, build

As YAML for a pack file

  - {term: build, theme_kind: version, surfaces: [b, build]}

Section page ›

Dictionary word

by

by · Core, connecting words

Kind: connective
Spelled: by

As YAML for a pack file

  - {term: by, theme_kind: connective, surfaces: [by]}

Section page ›

Dictionary word

byte

byte · Core, units

Kind: unit
Spelled: B, byte, bytes

As YAML for a pack file

  - {term: byte, theme_kind: unit, surfaces: [B, byte, bytes], dimension: digital_size,
     base: byte, factor: 1.0, ucum: By}

Section page ›

Dictionary word

C or C++ header

c_header · Core, formats

Kind: format
Spelled: h, hh, hpp, hxx

As YAML for a pack file

  - {term: c_header, canonical: "C or C++ header", theme_kind: format, surfaces: [h, hh, hpp,
     hxx], extension_only: [h], program: true}

Section page ›

Dictionary word

C or C++ source

c_source · Core, formats

Kind: format
Spelled: c, cc, cpp, cxx

As YAML for a pack file

  - {term: c_source, canonical: "C or C++ source", theme_kind: format, surfaces: [c, cc, cpp,
     cxx], extension_only: [c, cc, cpp], program: true}

Section page ›

Dictionary word

CAD drawing

cad_drawing · Core, formats

Kind: format
Spelled: dwg

As YAML for a pack file

  - {term: cad_drawing, canonical: "CAD drawing", theme_kind: format, surfaces: [dwg]}

Section page ›

Dictionary word

CAD exchange

cad_exchange_format · Core, formats

Kind: format
Spelled: igs, iges, stp, step

As YAML for a pack file

  - {term: cad_exchange_format, canonical: "CAD exchange", theme_kind: format, surfaces: [igs,
     iges, stp, step], extension_only: [stp, step]}

Section page ›

Dictionary word

calibrated

calibrated · Core, process

Kind: stage
Spelled: cal, calib, calibrated, calibration

As YAML for a pack file

  - {term: calibrated, theme_kind: stage, surfaces: [cal, calib, calibrated, calibration]}

Section page ›

Dictionary word

calibration data

calibration_data · Core, file roles

Kind: file role
Spelled: calibration, calib, cal_file, calibrant, blank_ref

As YAML for a pack file

  - {term: calibration_data, theme_kind: file_role, surfaces: [calibration, calib, cal_file,
     calibrant, blank_ref]}

Section page ›

Dictionary word

calorie

calorie · Core, units

Kind: unit
Spelled: cal, calorie

As YAML for a pack file

  - {term: calorie, theme_kind: unit, surfaces: [cal, calorie], dimension: energy, base: joule,
     factor: 4.184, ucum: cal}

Section page ›

Dictionary word

camera

camera · Core, instruments

Kind: instrument
Spelled: camera, cam, detector, sensor, ccd, emccd, scmos, cmos

As YAML for a pack file

  - {term: camera, theme_kind: instrument, surfaces: [camera, cam, detector, sensor, ccd, emccd,
     scmos, cmos]}

Section page ›

Dictionary word

celsius

celsius · Core, units

Kind: unit
Spelled: C, degC, °C, celsius, centigrade

As YAML for a pack file

  - {term: celsius, theme_kind: unit, surfaces: [C, degC, "°C", celsius, centigrade],
     dimension: temperature, base: kelvin, factor: 1.0, offset: 273.15, ucum: Cel}

Section page ›

Dictionary word

centimetre

centimetre · Core, units

Kind: unit
Spelled: cm, centimetre, centimeter

As YAML for a pack file

  - {term: centimetre, theme_kind: unit, surfaces: [cm, centimetre, centimeter],
     dimension: length, base: metre, factor: 0.01, ucum: cm}

Section page ›

Dictionary word

centrifuge

centrifuge · Core, instruments

Kind: instrument
Spelled: centrifuge, ultracentrifuge, microfuge, spin

As YAML for a pack file

  - {term: centrifuge, theme_kind: instrument, surfaces: [centrifuge, ultracentrifuge, microfuge,
     spin]}

Section page ›

Dictionary word

certificate

certificate_format · Core, formats

Kind: format
Spelled: pem, crt, cer

As YAML for a pack file

  - {term: certificate_format, canonical: certificate, theme_kind: format, surfaces: [pem, crt,
     cer]}

Section page ›

Dictionary word

changelog

changelog · Core, file roles

Kind: file role
Spelled: changelog, changes, history, news, releasenotes

As YAML for a pack file

  - {term: changelog, theme_kind: file_role, surfaces: [changelog, changes, history, news,
     releasenotes]}

Section page ›

Dictionary word

check

check · Core, negative lexicon

Kind: quality
Spelled: check, checkme, verify, confirm, review, revisit, recheck, doublecheck

As YAML for a pack file

  - {term: check, theme_kind: quality, surfaces: [check, checkme, verify, confirm, review,
     revisit, recheck, doublecheck], strength: moderate}

Section page ›

Dictionary word

checksum

checksum · Core, process

Kind: process
Spelled: checksum, md5, sha1, sha256, hash, digest

As YAML for a pack file

  - {term: checksum, theme_kind: process, surfaces: [checksum, md5, sha1, sha256, hash, digest]}

Section page ›

Dictionary word

chi square

chi_square · Core, statistics

Kind: statistic
Spelled: chisq, chisquare, chi-square, chi2

As YAML for a pack file

  - {term: chi_square, theme_kind: statistic, surfaces: [chisq, chisquare, "chi-square", chi2]}

Section page ›

Dictionary word

citation records

citation_format · Core, formats

Kind: format
Spelled: ris, nbib, bibtex, enw

As YAML for a pack file

  - {term: citation_format, canonical: "citation records", theme_kind: format, surfaces: [ris,
     nbib, bibtex, enw]}

Section page ›

Dictionary word

Clojure source

clojure_source · Core, formats

Kind: format
Spelled: clj

As YAML for a pack file

  - {term: clojure_source, canonical: "Clojure source", theme_kind: format, surfaces: [clj],
     program: true}

Section page ›

Dictionary word

clustering

clustering · Core, statistics

Kind: statistic
Spelled: cluster, clusters, clustering, kmeans, hierarchical, dbscan, hdbscan, louvain and 1 more

As YAML for a pack file

  - {term: clustering, theme_kind: statistic, surfaces: [cluster, clusters, clustering, kmeans,
     hierarchical, dbscan, hdbscan, louvain, leiden]}

Section page ›

Dictionary word

coefficient

coefficient · Core, statistics

Kind: statistic
Spelled: coef, coeff, coefficient, beta, weight

As YAML for a pack file

  - {term: coefficient, theme_kind: statistic, surfaces: [coef, coeff, coefficient, beta,
     weight]}

Section page ›

Dictionary word

coefficient of variation

coefficient_of_variation · Core, statistics

Kind: statistic
Spelled: cv, coefficient-of-variation

As YAML for a pack file

  - {term: coefficient_of_variation, theme_kind: statistic, surfaces: [cv,
     "coefficient-of-variation"]}

Section page ›

Dictionary word

complete

complete · Core, process

Kind: status
Spelled: complete, completed, done, finished, success, ok, passed

As YAML for a pack file

  - {term: complete, theme_kind: status, surfaces: [complete, completed, done, finished, success,
     ok, passed]}

Section page ›

Dictionary word

compressed

compressed · Core, process

Kind: stage
Spelled: compressed, zipped, gzipped, packed

As YAML for a pack file

  - {term: compressed, theme_kind: stage, surfaces: [compressed, zipped, gzipped, packed]}

Section page ›

Dictionary word

compressed archive

compressed_archive · Core, formats

Kind: format
Spelled: tar.gz, tar.bz2, tar.xz, tar.zst, tgz, tbz2

As YAML for a pack file

  - {term: compressed_archive, canonical: "compressed archive", theme_kind: format,
     surfaces: ["tar.gz", "tar.bz2", "tar.xz", "tar.zst", tgz, tbz2]}

Section page ›

Dictionary word

compressed stream

compression_format · Core, formats

Kind: format
Spelled: gz, bz2, zst, lz4
Ambiguous: Yes. Also read as orthogonal view

As YAML for a pack file

  - {term: compression_format, canonical: "compressed stream", theme_kind: format, surfaces: [gz,
     bz2, zst, lz4], ambiguous_with: [orthogonal_view], wraps: true}

Section page ›

Dictionary word

condition

condition · Core, process

Kind: condition
Spelled: cond, condition, conditions

As YAML for a pack file

  - {term: condition, theme_kind: condition, surfaces: [cond, condition, conditions]}

Section page ›

Dictionary word

confidence interval

confidence_interval · Core, statistics

Kind: statistic
Spelled: ci, confidence-interval, ci95, lower, upper, bounds

As YAML for a pack file

  - {term: confidence_interval, theme_kind: statistic, surfaces: [ci, "confidence-interval",
     ci95, lower, upper, bounds]}

Section page ›

Dictionary word

configuration

configuration · Core, process

Kind: process
Spelled: config, cfg, conf, settings, params, parameters, options, opts

As YAML for a pack file

  - {term: configuration, theme_kind: process, surfaces: [config, cfg, conf, settings, params,
     parameters, options, opts]}

Section page ›

Dictionary word

configuration file

configuration_file · Core, formats

Kind: format
Spelled: conf, cnf, cfg, config, properties, plist

As YAML for a pack file

  - {term: configuration_file, canonical: "configuration file", theme_kind: format,
     surfaces: [conf, cnf, cfg, config, properties, plist], extension_only: [cfg, conf, config,
     properties, plist]}

Section page ›

Dictionary word

conflicted

conflicted · Core, negative lexicon

Kind: quality
Spelled: conflict, conflicted, conflicted-copy, mergeconflict, sync_conflict

As YAML for a pack file

  - {term: conflicted, theme_kind: quality, surfaces: [conflict, conflicted, "conflicted-copy",
     mergeconflict, sync_conflict], strength: strong,
     note: "Cloud sync services write this. It means two versions diverged and neither won."}

Section page ›

Dictionary word

confusion matrix

confusion_matrix · Core, statistics

Kind: statistic
Spelled: confusion, tp, fp, tn, fn

As YAML for a pack file

  - {term: confusion_matrix, theme_kind: statistic, surfaces: [confusion, tp, fp, tn, fn]}

Section page ›

Dictionary word

contaminated

contaminated · Core, negative lexicon

Kind: quality
Spelled: contaminated, contamination, contam, dirty, infected

As YAML for a pack file

  - {term: contaminated, theme_kind: quality, surfaces: [contaminated, contamination, contam,
     dirty, infected], strength: strong}

Section page ›

Dictionary word

control

control · Core, process

Kind: condition
Spelled: ctrl, ctl, control, controls, untreated, mock, sham

As YAML for a pack file

  - {term: control, theme_kind: condition, surfaces: [ctrl, ctl, control, controls, untreated,
     mock, sham]}

Section page ›

Dictionary word

converted

converted · Core, process

Kind: stage
Spelled: conv, converted, conversion, transcoded, reformatted

As YAML for a pack file

  - {term: converted, theme_kind: stage, surfaces: [conv, converted, conversion, transcoded,
     reformatted]}

Section page ›

Dictionary word

copy

copy · Core, time and versions

Kind: version
Spelled: copy, duplicate, dup, clone

As YAML for a pack file

  - {term: copy, theme_kind: version, surfaces: [copy, duplicate, dup, clone]}

Section page ›

Dictionary word

corrected

corrected · Core, process

Kind: stage
Spelled: corr, corrected, correction, adjusted

As YAML for a pack file

  - {term: corrected, theme_kind: stage, surfaces: [corr, corrected, correction, adjusted]}

Section page ›

Dictionary word

correlation

correlation · Core, statistics

Kind: statistic
Spelled: corr, correlation, pearson, spearman, kendall, rho, tau

As YAML for a pack file

  - {term: correlation, theme_kind: statistic, surfaces: [corr, correlation, pearson, spearman,
     kendall, rho, tau]}

Section page ›

Dictionary word

correspondence

correspondence · Core, file roles

Kind: file role
Spelled: email, letter, correspondence, message, reply

As YAML for a pack file

  - {term: correspondence, theme_kind: file_role, surfaces: [email, letter, correspondence,
     message, reply]}

Section page ›

Dictionary word

count

count · Core, statistics

Kind: statistic
Spelled: n, count, counts, number, freq, frequency, tally
Ambiguous: Yes. Also read as stated replicate count

As YAML for a pack file

  - {term: count, theme_kind: statistic, surfaces: ["n", count, counts, number, freq, frequency,
     tally], ambiguous_with: [stated_replicate_count]}

Section page ›

Dictionary word

cropped

cropped · Core, process

Kind: stage
Spelled: crop, cropped, cropping, trimmed

As YAML for a pack file

  - {term: cropped, theme_kind: stage, surfaces: [crop, cropped, cropping, trimmed]}

Section page ›

Dictionary word

cross validation

cross_validation · Core, statistics

Kind: statistic
Spelled: cv_fold, crossval, kfold, holdout, train, test, validation, val

As YAML for a pack file

  - {term: cross_validation, theme_kind: statistic, surfaces: [cv_fold, crossval, kfold, holdout,
     train, test, validation, val]}

Section page ›

Dictionary word

cumulative distribution

cumulative_distribution · Core, file roles

Kind: file role
Spelled: cdf, ecdf

As YAML for a pack file

  - {term: cumulative_distribution, theme_kind: file_role, surfaces: [cdf, ecdf], product: true}

Section page ›

Dictionary word

curie

curie · Core, units

Kind: unit
Spelled: Ci, curie

As YAML for a pack file

  - {term: curie, theme_kind: unit, surfaces: [Ci, curie], dimension: radioactivity,
     base: becquerel, factor: "3.7e10", ucum: Ci}

Section page ›

Dictionary word

cytometer

cytometer · Core, instruments

Kind: instrument
Spelled: cytometer, flowcytometer, facs, sorter, cellsorter

As YAML for a pack file

  - {term: cytometer, theme_kind: instrument, surfaces: [cytometer, flowcytometer, facs, sorter,
     cellsorter]}

Section page ›

Dictionary word

dalton

dalton · Core, units

Kind: unit
Spelled: Da, dalton, daltons, amu

As YAML for a pack file

  - {term: dalton, theme_kind: unit, surfaces: [Da, dalton, daltons, amu],
     dimension: molecular_mass, base: dalton, factor: 1.0, ucum: u}

Section page ›

Dictionary word

database table file

database_table_file · Core, formats

Kind: format
Spelled: frm, myd, myi, opt

As YAML for a pack file

  - {term: database_table_file, canonical: "database table file", theme_kind: format,
     surfaces: [frm, myd, myi, opt], extension_only: [frm, myd, myi, opt]}

Section page ›

Dictionary word

dataset

dataset · Core, process

Kind: dataset
Spelled: dataset, datasets, data, ds

As YAML for a pack file

  - {term: dataset, theme_kind: dataset, surfaces: [dataset, datasets, data, ds]}

Section page ›

Dictionary word

day

day · Core, units

Kind: unit
Spelled: d, day, days, dpi, dpf
Ambiguous: Yes. Also read as dots per inch

As YAML for a pack file

  - {term: day, theme_kind: unit, surfaces: [d, day, days, dpi, dpf], dimension: time,
     base: second, factor: 86400.0, ambiguous_with: [dots_per_inch], ucum: d}

Section page ›

Dictionary word

debug

debug · Core, negative lexicon

Kind: quality
Spelled: debug, debugging, dbg, verbose_out, tracefile

As YAML for a pack file

  - {term: debug, theme_kind: quality, surfaces: [debug, debugging, dbg, verbose_out, tracefile],
     strength: moderate}

Section page ›

Dictionary word

december

december · Core, time and versions

Kind: date
Canonical: 12
Spelled: dec, december

As YAML for a pack file

  - {term: december, canonical: "12", theme_kind: date, surfaces: [dec, december]}

Section page ›

Dictionary word

deconvolved

deconvolved · Core, process

Kind: stage
Spelled: decon, deconv, deconvolved, deconvolution

As YAML for a pack file

  - {term: deconvolved, theme_kind: stage, surfaces: [decon, deconv, deconvolved,
     deconvolution]}

Section page ›

Dictionary word

default name

default_name · Core, negative lexicon

Kind: quality
Spelled: document1, document2, book1, sheet1, presentation1, image1, newfile, new-file

As YAML for a pack file

  - {term: default_name, theme_kind: quality, surfaces: [document1, document2, book1, sheet1,
     presentation1, image1, newfile, "new-file"], strength: strong}

Section page ›

Dictionary word

degree

degree · Core, units

Kind: unit
Spelled: deg, °, degree, degrees

As YAML for a pack file

  - {term: degree, theme_kind: unit, surfaces: [deg, "°", degree, degrees], dimension: angle,
     base: degree, factor: 1.0, ucum: deg}

Section page ›

Dictionary word

delete

delete · Core, negative lexicon

Kind: quality
Spelled: delete, deleteme, delete-me, todelete, toremove, removeme, trash, bin and 1 more

As YAML for a pack file

  - {term: delete, theme_kind: quality, surfaces: [delete, deleteme, "delete-me", todelete,
     toremove, removeme, trash, bin, recycle], strength: decisive}

Section page ›

Dictionary word

dendrogram

dendrogram · Core, statistics

Kind: statistic
Spelled: dendrogram, linkage, tree_plot

As YAML for a pack file

  - {term: dendrogram, theme_kind: statistic, surfaces: [dendrogram, linkage, tree_plot]}

Section page ›

Dictionary word

denoised

denoised · Core, process

Kind: stage
Spelled: denoised, denoise, denoising, noisereduced

As YAML for a pack file

  - {term: denoised, theme_kind: stage, surfaces: [denoised, denoise, denoising, noisereduced]}

Section page ›

Dictionary word

density plot

density_plot · Core, file roles

Kind: file role
Spelled: kde, gkde, densityplot, density-plot

As YAML for a pack file

  - {term: density_plot, theme_kind: file_role, surfaces: [kde, gkde, densityplot,
     "density-plot"], product: true}

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Dictionary word

deprecated

deprecated · Core, negative lexicon

Kind: quality
Spelled: deprecated, deprec, superseded, retired, defunct

As YAML for a pack file

  - {term: deprecated, theme_kind: quality, surfaces: [deprecated, deprec, superseded, retired,
     defunct], strength: decisive}

Section page ›

Dictionary word

dictionary file

dictionary_file · Core, file roles

Kind: file role
Spelled: dictionary, glossary, codebook, lookup, mapping, keyfile, legend, key

As YAML for a pack file

  - {term: dictionary_file, theme_kind: file_role, surfaces: [dictionary, glossary, codebook,
     lookup, mapping, keyfile, legend, key]}

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Dictionary word

difference

difference · Core, statistics

Kind: statistic
Spelled: diff, difference, delta, change

As YAML for a pack file

  - {term: difference, theme_kind: statistic, surfaces: [diff, difference, delta, change]}

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Dictionary word

diffusion coefficient

diffusion_coefficient · Core, statistics

Kind: statistic
Spelled: deff, d_eff, diffusion_coefficient, diffusion-coefficient, diffusivity

As YAML for a pack file

  - {term: diffusion_coefficient, theme_kind: statistic, surfaces: [deff, d_eff,
     diffusion_coefficient, "diffusion-coefficient", diffusivity]}

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Dictionary word

dimensionality reduction

dimensionality_reduction · Core, statistics

Kind: statistic
Spelled: tsne, t-sne, umap, lda, ica, nmf, mds, embedding

As YAML for a pack file

  - {term: dimensionality_reduction, theme_kind: statistic, surfaces: [tsne, "t-sne", umap, lda,
     ica, nmf, mds, embedding]}

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Dictionary word

distance

distance · Core, statistics

Kind: statistic
Spelled: dist, distance, euclidean, cosine, jaccard, manhattan, mahalanobis

As YAML for a pack file

  - {term: distance, theme_kind: statistic, surfaces: [dist, distance, euclidean, cosine,
     jaccard, manhattan, mahalanobis]}

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Dictionary word

do not analyse

do_not_analyse · Core, negative lexicon

Kind: quality
Spelled: donotanalyse, do-not-analyse, do_not_analyse, donotanalyze, do-not-analyze, do_not_analyze, notforanalysis, excludefromanalysis

As YAML for a pack file

  - {term: do_not_analyse, theme_kind: quality, surfaces: [donotanalyse, "do-not-analyse",
     do_not_analyse, donotanalyze, "do-not-analyze", do_not_analyze, notforanalysis,
     excludefromanalysis], strength: decisive}

Section page ›

Dictionary word

do not use

do_not_use · Core, negative lexicon

Kind: quality
Spelled: donotuse, do-not-use, do_not_use, dontuse, dont-use, notuse, unusable

As YAML for a pack file

  - {term: do_not_use, theme_kind: quality, surfaces: [donotuse, "do-not-use", do_not_use,
     dontuse, "dont-use", notuse, unusable], strength: decisive}

Section page ›

Dictionary word

dots per inch

dots_per_inch · Core, units

Kind: unit
Spelled: dpi, DPI, ppi
Ambiguous: Yes. Also read as day

As YAML for a pack file

  - {term: dots_per_inch, theme_kind: unit, surfaces: [dpi, DPI, ppi], dimension: resolution,
     base: dpi, factor: 1.0, ambiguous_with: [day]}

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Dictionary word

downsampled

downsampled · Core, process

Kind: stage
Spelled: downsampled, downsample, decimated, subsampled

As YAML for a pack file

  - {term: downsampled, theme_kind: stage, surfaces: [downsampled, downsample, decimated,
     subsampled]}

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Dictionary word

draft

draft · Core, time and versions

Kind: version
Spelled: draft, drafts, wip, work-in-progress

As YAML for a pack file

  - {term: draft, theme_kind: version, surfaces: [draft, drafts, wip, "work-in-progress"]}

Section page ›

Dictionary word

dummy

dummy · Core, negative lexicon

Kind: quality
Spelled: dummy, placeholder, stub, fake, mock_data, synthetic_placeholder, lorem

As YAML for a pack file

  - {term: dummy, theme_kind: quality, surfaces: [dummy, placeholder, stub, fake, mock_data,
     synthetic_placeholder, lorem], strength: strong}

Section page ›

Dictionary word

duplicate

duplicate · Core, negative lexicon

Kind: quality
Spelled: dup, dupe, duplicate, copy2, copy3, copy-of, copyof, (1) and 2 more

As YAML for a pack file

  - {term: duplicate, theme_kind: quality, surfaces: [dup, dupe, duplicate, copy2, copy3,
     "copy-of", copyof, "(1)", "(2)", "- Copy"], strength: moderate}

Section page ›

Dictionary word

editor backup

editor_backup · Core, filesystem noise

Kind: quality
Spelled: ~$, .swp, .swo, .bak~, #autosave#, .~lock

As YAML for a pack file

  - {term: editor_backup, theme_kind: quality, surfaces: ["~$", ".swp", ".swo", ".bak~",
     "#autosave#", ".~lock"], strength: decisive}

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Dictionary word

electronvolt

electronvolt · Core, units

Kind: unit
Spelled: eV, electronvolt

As YAML for a pack file

  - {term: electronvolt, theme_kind: unit, surfaces: [eV, electronvolt], dimension: energy,
     base: joule, factor: 1.602176634e-19, ucum: eV}

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Dictionary word

embedded database

embedded_database · Core, formats

Kind: format
Spelled: sqlite, duckdb, db

As YAML for a pack file

  - {term: embedded_database, canonical: "embedded database", theme_kind: format,
     surfaces: [sqlite, duckdb, db]}

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Dictionary word

emphatic

emphatic · Core, negative lexicon

Kind: quality
Spelled: ACTUAL, REAL, PROPER, DEFINITELY, PLEASE, IMPORTANT

As YAML for a pack file

  - {term: emphatic, theme_kind: quality, surfaces: [ACTUAL, REAL, PROPER, DEFINITELY, PLEASE,
     IMPORTANT], strength: moderate,
     note: "Capitalised emphasis in a filename is a person shouting at their future self."}

Section page ›

Dictionary word

environment

environment_file · Core, formats

Kind: format
Spelled: env, envrc

As YAML for a pack file

  - {term: environment_file, canonical: environment, theme_kind: format, surfaces: [env, envrc]}

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Dictionary word

error output

error_stream · Core, formats

Kind: format
Spelled: err, stderr

As YAML for a pack file

  - {term: error_stream, canonical: "error output", theme_kind: format, surfaces: [err, stderr],
     extension_only: [stderr]}

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Dictionary word

example

example · Core, negative lexicon

Kind: quality
Spelled: example, demo, sample_file, toy, tutorial

As YAML for a pack file

  - {term: example, theme_kind: quality, surfaces: [example, demo, sample_file, toy, tutorial],
     strength: moderate, ambiguous: true}

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Dictionary word

excluded

excluded · Core, negative lexicon

Kind: quality
Spelled: excluded, exclude, omitted, dropped, discarded, rejected, outlier, outliers

As YAML for a pack file

  - {term: excluded, theme_kind: quality, surfaces: [excluded, exclude, omitted, dropped,
     discarded, rejected, outlier, outliers], strength: moderate,
     note: "Deliberate exclusion, not doubt. Worth surfacing because the reason is rarely recorded anywhere else."}

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Dictionary word

executable

executable_format · Core, formats

Kind: format
Spelled: exe, dll, dylib, so, cpl

As YAML for a pack file

  - {term: executable_format, canonical: executable, theme_kind: format, surfaces: [exe, dll,
     dylib, so, cpl], extension_only: [cpl], program: true}

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Dictionary word

experiment

experiment · Core, process

Kind: experiment
Spelled: exp, expt, experiment, experiments

As YAML for a pack file

  - {term: experiment, theme_kind: experiment, surfaces: [exp, expt, experiment, experiments]}

Section page ›

Dictionary word

exponential

exponential · Core, statistics

Kind: statistic
Spelled: exp_fit, exponential, decay, growth

As YAML for a pack file

  - {term: exponential, theme_kind: statistic, surfaces: [exp_fit, exponential, decay, growth]}

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Dictionary word

export

export · Core, process

Kind: stage
Spelled: export, exported, exports, published, shared, delivery, deliverable

As YAML for a pack file

  - {term: export, theme_kind: stage, surfaces: [export, exported, exports, published, shared,
     delivery, deliverable]}

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Dictionary word

f score

f_score · Core, statistics

Kind: statistic
Spelled: f1, fscore, f-score, fbeta

As YAML for a pack file

  - {term: f_score, theme_kind: statistic, surfaces: [f1, fscore, "f-score", fbeta]}

Section page ›

Dictionary word

fahrenheit

fahrenheit · Core, units

Kind: unit
Spelled: degF, °F, fahrenheit

As YAML for a pack file

  - {term: fahrenheit, theme_kind: unit, surfaces: [degF, "°F", fahrenheit],
     dimension: temperature, base: kelvin, factor: 0.5555555555555556, offset: 255.3722222222222,
     ucum: "[degF]"}

Section page ›

Dictionary word

failed

failed · Core, negative lexicon

Kind: quality
Spelled: failed, failure, fail, crashed, aborted, died

As YAML for a pack file

  - {term: failed, theme_kind: quality, surfaces: [failed, failure, fail, crashed, aborted,
     died], strength: strong}

Section page ›

Dictionary word

failed run

failed_run · Core, process

Kind: status
Spelled: error, errored

As YAML for a pack file

  - {term: failed_run, theme_kind: status, surfaces: [error, errored]}

Section page ›

Dictionary word

farad

farad · Core, units

Kind: unit
Spelled: F, farad

As YAML for a pack file

  - {term: farad, theme_kind: unit, surfaces: [F, farad], dimension: capacitance, base: farad,
     factor: 1.0, ucum: F}

Section page ›

Dictionary word

february

february · Core, time and versions

Kind: date
Canonical: 02
Spelled: feb, february

As YAML for a pack file

  - {term: february, canonical: "02", theme_kind: date, surfaces: [feb, february]}

Section page ›

Dictionary word

femtogram

femtogram · Core, units

Kind: unit
Spelled: fg, femtogram

As YAML for a pack file

  - {term: femtogram, theme_kind: unit, surfaces: [fg, femtogram], dimension: mass, base: gram,
     factor: 1.0e-15, ucum: fg}

Section page ›

Dictionary word

femtomolar

femtomolar · Core, units

Kind: unit
Spelled: fM, femtomolar

As YAML for a pack file

  - {term: femtomolar, theme_kind: unit, surfaces: [fM, femtomolar], dimension: concentration,
     base: molar, factor: 1.0e-15, ucum: "fmol/L"}

Section page ›

Dictionary word

femtomole

femtomole · Core, units

Kind: unit
Spelled: fmol, femtomole

As YAML for a pack file

  - {term: femtomole, theme_kind: unit, surfaces: [fmol, femtomole], dimension: amount,
     base: mole, factor: 1.0e-15, ucum: fmol}

Section page ›

Dictionary word

figure

figure · Core, file roles

Kind: file role
Spelled: fig, figure, figures, panel, panels, plate_figure, graphic

As YAML for a pack file

  - {term: figure, theme_kind: file_role, surfaces: [fig, figure, figures, panel, panels,
     plate_figure, graphic], product: true}

Section page ›

Dictionary word

filter

filter · Core, instruments

Kind: instrument
Spelled: filter, filters, filterset, dichroic, emission_filter, excitation_filter, bandpass, longpass and 1 more

As YAML for a pack file

  - {term: filter, theme_kind: instrument, surfaces: [filter, filters, filterset, dichroic,
     emission_filter, excitation_filter, bandpass, longpass, shortpass]}

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Dictionary word

filtered

filtered · Core, process

Kind: stage
Spelled: filt, filtered, filtering

As YAML for a pack file

  - {term: filtered, theme_kind: stage, surfaces: [filt, filtered, filtering]}

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Dictionary word

final

final · Core, time and versions

Kind: version
Spelled: final, fin, finished

As YAML for a pack file

  - {term: final, theme_kind: version, surfaces: [final, fin, finished]}

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Dictionary word

final final

final_final · Core, negative lexicon

Kind: quality
Spelled: finalfinal, final_final, final-final, finalfinalfinal, reallyfinal, actualfinal, truefinal

As YAML for a pack file

  - {term: final_final, theme_kind: quality, surfaces: [finalfinal, final_final, "final-final",
     finalfinalfinal, reallyfinal, actualfinal, truefinal], strength: decisive}

Section page ›

Dictionary word

fisher exact

fisher_exact · Core, statistics

Kind: statistic
Spelled: fisher, fishers, fisher-exact

As YAML for a pack file

  - {term: fisher_exact, theme_kind: statistic, surfaces: [fisher, fishers, "fisher-exact"]}

Section page ›

Dictionary word

fit

fit · Core, statistics

Kind: statistic
Spelled: fit, fitted, fitting, model, modelled, modeled

As YAML for a pack file

  - {term: fit, theme_kind: statistic, surfaces: [fit, fitted, fitting, model, modelled,
     modeled]}

Section page ›

Dictionary word

fixme

fixme · Core, negative lexicon

Kind: quality
Spelled: fixme, fix-me, tofix, needsfix, broken_fix, hack, kludge, workaround

As YAML for a pack file

  - {term: fixme, theme_kind: quality, surfaces: [fixme, "fix-me", tofix, needsfix, broken_fix,
     hack, kludge, workaround], strength: strong}

Section page ›

Dictionary word

fold

fold · Core, units

Kind: unit
Spelled: x, X, fold, -fold
Ambiguous: Yes. Also read as magnification

As YAML for a pack file

  - {term: fold, theme_kind: unit, surfaces: [x, X, fold, "-fold"], dimension: multiple,
     base: fold, factor: 1.0, ambiguous_with: [magnification]}

Section page ›

Dictionary word

fold change

fold_change · Core, statistics

Kind: statistic
Spelled: fc, foldchange, fold-change, log2fc, logfc

As YAML for a pack file

  - {term: fold_change, theme_kind: statistic, surfaces: [fc, foldchange, "fold-change", log2fc,
     logfc]}

Section page ›

Dictionary word

font

font_format · Core, formats

Kind: format
Spelled: ttf, otf, woff, woff2

As YAML for a pack file

  - {term: font_format, canonical: font, theme_kind: format, surfaces: [ttf, otf, woff, woff2]}

Section page ›

Dictionary word

foot

foot · Core, units

Kind: unit
Spelled: ft, foot, feet

As YAML for a pack file

  - {term: foot, theme_kind: unit, surfaces: [ft, foot, feet], dimension: length, base: metre,
     factor: 0.3048, ucum: "[ft_i]"}

Section page ›

Dictionary word

for

for · Core, connecting words

Kind: connective
Spelled: for

As YAML for a pack file

  - {term: for, theme_kind: connective, surfaces: [for]}

Section page ›

Dictionary word

Fortran module

fortran_module · Core, formats

Kind: format
Spelled: mod

As YAML for a pack file

  - {term: fortran_module, canonical: "Fortran module", theme_kind: format, surfaces: [mod],
     extension_only: [mod], program: true}

Section page ›

Dictionary word

frame

frame · Core, process

Kind: part
Spelled: frame, frames

As YAML for a pack file

  - {term: frame, theme_kind: part, surfaces: [frame, frames]}

Section page ›

Dictionary word

frames per second

frames_per_second · Core, units

Kind: unit
Spelled: fps, FPS

As YAML for a pack file

  - {term: frames_per_second, theme_kind: unit, surfaces: [fps, FPS], dimension: frame_rate,
     base: fps, factor: 1.0}

Section page ›

Dictionary word

freezer

freezer · Core, instruments

Kind: instrument
Spelled: freezer, fridge, minus80, -80, -20, ln2, cryostore, dewar

As YAML for a pack file

  - {term: freezer, theme_kind: instrument, surfaces: [freezer, fridge, minus80, "-80", "-20",
     ln2, cryostore, dewar]}

Section page ›

Dictionary word

friday

friday · Core, time and versions

Kind: date
Spelled: friday

As YAML for a pack file

  - {term: friday, theme_kind: date, surfaces: [friday], weekday: 5, stamp_abbreviation: fri}

Section page ›

Dictionary word

from

from · Core, connecting words

Kind: connective
Spelled: from

As YAML for a pack file

  - {term: from, theme_kind: connective, surfaces: [from]}

Section page ›

Dictionary word

gaussian

gaussian · Core, statistics

Kind: statistic
Spelled: gaussian, normal, lorentzian, voigt

As YAML for a pack file

  - {term: gaussian, theme_kind: statistic, surfaces: [gaussian, normal, lorentzian, voigt]}

Section page ›

Dictionary word

gel documentation

gel_documentation · Core, instruments

Kind: instrument
Spelled: geldoc, gel-doc, imager, licor, chemidoc, blotimager

As YAML for a pack file

  - {term: gel_documentation, theme_kind: instrument, surfaces: [geldoc, "gel-doc", imager,
     licor, chemidoc, blotimager]}

Section page ›

Dictionary word

gibibyte

gibibyte · Core, units

Kind: unit
Spelled: GiB, gibibyte

As YAML for a pack file

  - {term: gibibyte, theme_kind: unit, surfaces: [GiB, gibibyte], dimension: digital_size,
     base: byte, factor: 1073741824.0, ucum: GiBy}

Section page ›

Dictionary word

gigabyte

gigabyte · Core, units

Kind: unit
Spelled: GB, gigabyte

As YAML for a pack file

  - {term: gigabyte, theme_kind: unit, surfaces: [GB, gigabyte], dimension: digital_size,
     base: byte, factor: "1.0e9", ucum: GBy}

Section page ›

Dictionary word

gigahertz

gigahertz · Core, units

Kind: unit
Spelled: GHz, gigahertz

As YAML for a pack file

  - {term: gigahertz, theme_kind: unit, surfaces: [GHz, gigahertz], dimension: frequency,
     base: hertz, factor: "1.0e9", ucum: GHz}

Section page ›

Dictionary word

gigaohm

gigaohm · Core, units

Kind: unit
Spelled: Gohm, GΩ, gigaohm

As YAML for a pack file

  - {term: gigaohm, theme_kind: unit, surfaces: [Gohm, "GΩ", gigaohm], dimension: resistance,
     base: ohm, factor: "1.0e9", ucum: GOhm}

Section page ›

Dictionary word

gram

gram · Core, units

Kind: unit
Spelled: g, gram, grams, gm

As YAML for a pack file

  - {term: gram, theme_kind: unit, surfaces: [g, gram, grams, gm], dimension: mass, base: gram,
     factor: 1.0, ucum: g}

Section page ›

Dictionary word

gray

gray · Core, units

Kind: unit
Spelled: Gy, gray

As YAML for a pack file

  - {term: gray, theme_kind: unit, surfaces: [Gy, gray], dimension: absorbed_dose, base: gray,
     factor: 1.0, ucum: Gy}

Section page ›

Dictionary word

Groovy script

groovy_script · Core, formats

Kind: format
Spelled: groovy

As YAML for a pack file

  - {term: groovy_script, canonical: "Groovy script", theme_kind: format, surfaces: [groovy],
     extension_only: [groovy], program: true}

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Dictionary word

group

group · Core, process

Kind: condition
Spelled: group, groups, arm, arms, cohort, cohorts

As YAML for a pack file

  - {term: group, theme_kind: condition, surfaces: [group, groups, arm, arms, cohort, cohorts]}

Section page ›

Dictionary word

heatmap

heatmap · Core, file roles

Kind: file role
Spelled: heatmap, heatmaps, heat-map, heat_map

As YAML for a pack file

  - {term: heatmap, theme_kind: file_role, surfaces: [heatmap, heatmaps, "heat-map", heat_map],
     product: true}

Section page ›

Dictionary word

hertz

hertz · Core, units

Kind: unit
Spelled: Hz, hertz

As YAML for a pack file

  - {term: hertz, theme_kind: unit, surfaces: [Hz, hertz], dimension: frequency, base: hertz,
     factor: 1.0, ucum: Hz}

Section page ›

Dictionary word

histogram

histogram · Core, file roles

Kind: file role
Spelled: histogram, histograms, hist

As YAML for a pack file

  - {term: histogram, theme_kind: file_role, surfaces: [histogram, histograms, hist],
     product: true}

Section page ›

Dictionary word

holm

holm · Core, statistics

Kind: statistic
Spelled: holm, sidak

As YAML for a pack file

  - {term: holm, theme_kind: statistic, surfaces: [holm, sidak]}

Section page ›

Dictionary word

hour

hour · Core, units

Kind: unit
Spelled: h, hr, hrs, hour, hours

As YAML for a pack file

  - {term: hour, theme_kind: unit, surfaces: [h, hr, hrs, hour, hours], dimension: time,
     base: second, factor: 3600.0, ucum: h}

Section page ›

Dictionary word

icon

icon_format · Core, formats

Kind: format
Spelled: ico, icns

As YAML for a pack file

  - {term: icon_format, canonical: icon, theme_kind: format, surfaces: [ico, icns]}

Section page ›

Dictionary word

ignore

ignore · Core, negative lexicon

Kind: quality
Spelled: ignore, ignored, ignoreme, disregard, skipme

As YAML for a pack file

  - {term: ignore, theme_kind: quality, surfaces: [ignore, ignored, ignoreme, disregard, skipme],
     strength: decisive}

Section page ›

Dictionary word

Illustrator document

illustrator_document · Core, formats

Kind: format
Spelled: ai

As YAML for a pack file

  - {term: illustrator_document, canonical: "Illustrator document", theme_kind: format,
     surfaces: [ai], extension_only: [ai], product: true}

Section page ›

Dictionary word

image

image · Core, file roles

Kind: file role
Spelled: image, images, img, picture, pic, photo, photograph, snapshot and 1 more

As YAML for a pack file

  - {term: image, theme_kind: file_role, surfaces: [image, images, img, picture, pic, photo,
     photograph, snapshot, screenshot]}

Section page ›

Dictionary word

image format

image_format · Core, formats

Kind: format
Spelled: tif, tiff, ometiff, ome-tiff, ome.tif, ome.tiff, png, jpg and 31 more

As YAML for a pack file

  - {term: image_format, theme_kind: format, surfaces: [tif, tiff, ometiff, "ome-tiff",
     "ome.tif", "ome.tiff", png, jpg, jpeg, jp2, bmp, gif, svg, eps, pdf_image, heic, heif, webp, emf,
     wmf, pgm, pbm, tga, nd2, czi, lif, oib, oif, lsm, ims, vsi, scn, ndpi, svs, dv, stk, fli, lifext,
     cr2], extension_only: [tga, lsm], origins: {nd2: {vendor: Nikon, written_by: instrument,
     accepts_pack: true}, czi: {vendor: Zeiss, written_by: instrument}, lsm: {vendor: Zeiss,
     written_by: instrument}, lif: {vendor: Leica, written_by: instrument}, lifext: {vendor: Leica,
     written_by: instrument}, scn: {vendor: "Leica or Bio-Rad", written_by: instrument},
     svs: {vendor: "Leica Aperio", written_by: instrument}, oib: {vendor: Olympus,
     written_by: instrument}, oif: {vendor: Olympus, written_by: instrument}, vsi: {vendor: Olympus,
     written_by: instrument}, ndpi: {vendor: Hamamatsu, written_by: instrument},
     dv: {vendor: "Applied Precision DeltaVision", written_by: instrument},
     stk: {vendor: "Molecular Devices MetaMorph", written_by: instrument},
     fli: {vendor: "Lambert Instruments", written_by: instrument},
     ims: {vendor: "Oxford Instruments Imaris", written_by: software}, cr2: {vendor: Canon,
     written_by: instrument}}}

Section page ›

Dictionary word

ImageJ macro

imagej_macro · Core, formats

Kind: format
Spelled: ijm

As YAML for a pack file

  - {term: imagej_macro, canonical: "ImageJ macro", theme_kind: format, surfaces: [ijm],
     program: true}

Section page ›

Dictionary word

inch

inch · Core, units

Kind: unit
Spelled: in, inch, inches, "

As YAML for a pack file

  - {term: inch, theme_kind: unit, surfaces: [in, inch, inches, "\""], dimension: length,
     base: metre, factor: 0.0254, ucum: "[in_i]"}

Section page ›

Dictionary word

incubator

incubator · Core, instruments

Kind: instrument
Spelled: incubator, incubation_chamber, co2, environmental_chamber, heated_stage

As YAML for a pack file

  - {term: incubator, theme_kind: instrument, surfaces: [incubator, incubation_chamber, co2,
     environmental_chamber, heated_stage]}

Section page ›

Dictionary word

INI

ini_document · Core, formats

Kind: format
Spelled: ini

As YAML for a pack file

  - {term: ini_document, canonical: INI, theme_kind: format, surfaces: [ini]}

Section page ›

Dictionary word

input data

input_data · Core, file roles

Kind: file role
Spelled: input, inputs

As YAML for a pack file

  - {term: input_data, theme_kind: file_role, surfaces: [input, inputs]}

Section page ›

Dictionary word

intercept

intercept · Core, statistics

Kind: statistic
Spelled: intercept, offset_term, b_coef

As YAML for a pack file

  - {term: intercept, theme_kind: statistic, surfaces: [intercept, offset_term, b_coef]}

Section page ›

Dictionary word

intermediate

intermediate · Core, process

Kind: stage
Spelled: intermediate, interim, working, scratch_stage, staging

As YAML for a pack file

  - {term: intermediate, theme_kind: stage, surfaces: [intermediate, interim, working,
     scratch_stage, staging]}

Section page ›

Dictionary word

interquartile range

interquartile_range · Core, statistics

Kind: statistic
Spelled: iqr

As YAML for a pack file

  - {term: interquartile_range, theme_kind: statistic, surfaces: [iqr]}

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Dictionary word

into

into · Core, connecting words

Kind: connective
Spelled: into

As YAML for a pack file

  - {term: into, theme_kind: connective, surfaces: [into]}

Section page ›

Dictionary word

invalid

invalid · Core, negative lexicon

Kind: quality
Spelled: invalid, bogus, nonsense, garbage, junk, rubbish_data

As YAML for a pack file

  - {term: invalid, theme_kind: quality, surfaces: [invalid, bogus, nonsense, garbage, junk,
     rubbish_data], strength: strong}

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Dictionary word

inventory file

inventory_file · Core, file roles

Kind: file role
Spelled: inventory, stock, registry, database_export, listing

As YAML for a pack file

  - {term: inventory_file, theme_kind: file_role, surfaces: [inventory, stock, registry,
     database_export, listing]}

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Dictionary word

iteration

iteration · Core, time and versions

Kind: replicate
Spelled: iter, iteration, iterations, epoch

As YAML for a pack file

  - {term: iteration, theme_kind: replicate, surfaces: [iter, iteration, iterations, epoch]}

Section page ›

Dictionary word

iWork document

iwork_document · Core, formats

Kind: format
Spelled: iwa, key, pages, numbers

As YAML for a pack file

  - {term: iwork_document, canonical: "iWork document", theme_kind: format, surfaces: [iwa, key,
     pages, numbers], extension_only: [key, pages, numbers], product: true}

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Dictionary word

january

january · Core, time and versions

Kind: date
Canonical: 01
Spelled: jan, january

As YAML for a pack file

  - {term: january, canonical: "01", theme_kind: date, surfaces: [jan, january]}

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Dictionary word

Java bytecode

java_bytecode · Core, formats

Kind: format
Spelled: class, jar

As YAML for a pack file

  - {term: java_bytecode, canonical: "Java bytecode", theme_kind: format, surfaces: [class, jar],
     extension_only: [class, jar], program: true}

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Dictionary word

Java source

java_source · Core, formats

Kind: format
Spelled: java, src

As YAML for a pack file

  - {term: java_source, canonical: "Java source", theme_kind: format, surfaces: [java, src],
     extension_only: [java, src], program: true}

Section page ›

Dictionary word

JavaScript

javascript_source · Core, formats

Kind: format
Spelled: js, mjs, cjs

As YAML for a pack file

  - {term: javascript_source, canonical: JavaScript, theme_kind: format, surfaces: [js, mjs,
     cjs], program: true}

Section page ›

Dictionary word

job

job · Core, process

Kind: process
Spelled: job, jobs, task, tasks

As YAML for a pack file

  - {term: job, theme_kind: process, surfaces: [job, jobs, task, tasks]}

Section page ›

Dictionary word

joule

joule · Core, units

Kind: unit
Spelled: J, joule, joules

As YAML for a pack file

  - {term: joule, theme_kind: unit, surfaces: [J, joule, joules], dimension: energy, base: joule,
     factor: 1.0, ucum: J}

Section page ›

Dictionary word

july

july · Core, time and versions

Kind: date
Canonical: 07
Spelled: jul, july

As YAML for a pack file

  - {term: july, canonical: "07", theme_kind: date, surfaces: [jul, july]}

Section page ›

Dictionary word

june

june · Core, time and versions

Kind: date
Canonical: 06
Spelled: jun, june

As YAML for a pack file

  - {term: june, canonical: "06", theme_kind: date, surfaces: [jun, june]}

Section page ›

Dictionary word

kelvin

kelvin · Core, units

Kind: unit
Spelled: K, kelvin

As YAML for a pack file

  - {term: kelvin, theme_kind: unit, surfaces: [K, kelvin], dimension: temperature, base: kelvin,
     factor: 1.0, ucum: K}

Section page ›

Dictionary word

keyboard mash

keyboard_mash · Core, negative lexicon

Kind: quality
Spelled: asdf, asdfasdf, qwerty, test123, foo, baz, blah

As YAML for a pack file

  - {term: keyboard_mash, theme_kind: quality, surfaces: [asdf, asdfasdf, qwerty, test123, foo,
     baz, blah], strength: low}

Section page ›

Dictionary word

kibibyte

kibibyte · Core, units

Kind: unit
Spelled: KiB, kibibyte

As YAML for a pack file

  - {term: kibibyte, theme_kind: unit, surfaces: [KiB, kibibyte], dimension: digital_size,
     base: byte, factor: 1024.0, ucum: KiBy}

Section page ›

Dictionary word

kilobyte

kilobyte · Core, units

Kind: unit
Spelled: KB, kB, kilobyte

As YAML for a pack file

  - {term: kilobyte, theme_kind: unit, surfaces: [KB, kB, kilobyte], dimension: digital_size,
     base: byte, factor: 1000.0, ucum: kBy}

Section page ›

Dictionary word

kilocalorie

kilocalorie · Core, units

Kind: unit
Spelled: kcal, kilocalorie, Cal

As YAML for a pack file

  - {term: kilocalorie, theme_kind: unit, surfaces: [kcal, kilocalorie, Cal], dimension: energy,
     base: joule, factor: 4184.0, ucum: kcal}

Section page ›

Dictionary word

kilodalton

kilodalton · Core, units

Kind: unit
Spelled: kDa, kilodalton

As YAML for a pack file

  - {term: kilodalton, theme_kind: unit, surfaces: [kDa, kilodalton], dimension: molecular_mass,
     base: dalton, factor: 1000.0, ucum: ku}

Section page ›

Dictionary word

kiloelectronvolt

kiloelectronvolt · Core, units

Kind: unit
Spelled: keV

As YAML for a pack file

  - {term: kiloelectronvolt, theme_kind: unit, surfaces: [keV], dimension: energy, base: joule,
     factor: 1.602176634e-16, ucum: keV}

Section page ›

Dictionary word

kilogram

kilogram · Core, units

Kind: unit
Spelled: kg, kilogram, kilograms

As YAML for a pack file

  - {term: kilogram, theme_kind: unit, surfaces: [kg, kilogram, kilograms], dimension: mass,
     base: gram, factor: 1000.0, ucum: kg}

Section page ›

Dictionary word

kilohertz

kilohertz · Core, units

Kind: unit
Spelled: kHz, kilohertz

As YAML for a pack file

  - {term: kilohertz, theme_kind: unit, surfaces: [kHz, kilohertz], dimension: frequency,
     base: hertz, factor: 1000.0, ucum: kHz}

Section page ›

Dictionary word

kilojoule

kilojoule · Core, units

Kind: unit
Spelled: kJ, kilojoule

As YAML for a pack file

  - {term: kilojoule, theme_kind: unit, surfaces: [kJ, kilojoule], dimension: energy,
     base: joule, factor: 1000.0, ucum: kJ}

Section page ›

Dictionary word

kilometre

kilometre · Core, units

Kind: unit
Spelled: km, kilometre, kilometer

As YAML for a pack file

  - {term: kilometre, theme_kind: unit, surfaces: [km, kilometre, kilometer], dimension: length,
     base: metre, factor: 1000.0, ucum: km}

Section page ›

Dictionary word

kilopascal

kilopascal · Core, units

Kind: unit
Spelled: kPa, kilopascal

As YAML for a pack file

  - {term: kilopascal, theme_kind: unit, surfaces: [kPa, kilopascal], dimension: pressure,
     base: pascal, factor: 1000.0, ucum: kPa}

Section page ›

Dictionary word

kolmogorov smirnov

kolmogorov_smirnov · Core, statistics

Kind: statistic
Spelled: ks, kstest, kolmogorov-smirnov

As YAML for a pack file

  - {term: kolmogorov_smirnov, theme_kind: statistic, surfaces: [ks, kstest,
     "kolmogorov-smirnov"]}

Section page ›

Dictionary word

kruskal wallis

kruskal_wallis · Core, statistics

Kind: statistic
Spelled: kruskal, kruskal-wallis

As YAML for a pack file

  - {term: kruskal_wallis, theme_kind: statistic, surfaces: [kruskal, "kruskal-wallis"]}

Section page ›

Dictionary word

kymograph

kymograph · Core, file roles

Kind: file role
Spelled: kymograph, kymographs, kymo

As YAML for a pack file

  - {term: kymograph, theme_kind: file_role, surfaces: [kymograph, kymographs, kymo],
     product: true}

Section page ›

Dictionary word

lamp

lamp · Core, instruments

Kind: instrument
Spelled: lamp, led, arc, halogen, xenon, mercury, illuminator

As YAML for a pack file

  - {term: lamp, theme_kind: instrument, surfaces: [lamp, led, arc, halogen, xenon, mercury,
     illuminator]}

Section page ›

Dictionary word

language cache

language_cache · Core, filesystem noise

Kind: quality
Spelled: __pycache__, .pyc, .pyo, .ipynb_checkpoints, .Rhistory, .RData, .Rproj.user, node_modules and 3 more

As YAML for a pack file

  - {term: language_cache, theme_kind: quality, surfaces: [__pycache__, ".pyc", ".pyo",
     ".ipynb_checkpoints", ".Rhistory", ".RData", ".Rproj.user", node_modules, ".mypy_cache",
     ".pytest_cache", ".ruff_cache"], strength: decisive}

Section page ›

Dictionary word

laser

laser · Core, instruments

Kind: instrument
Spelled: laser, lasers, laserline, excitation_source

As YAML for a pack file

  - {term: laser, theme_kind: instrument, surfaces: [laser, lasers, laserline,
     excitation_source]}

Section page ›

Dictionary word

latest

latest · Core, time and versions

Kind: version
Spelled: latest, current, newest, head

As YAML for a pack file

  - {term: latest, theme_kind: version, surfaces: [latest, current, newest, head]}

Section page ›

Dictionary word

LaTeX source

latex_source · Core, formats

Kind: format
Spelled: tex, latex

As YAML for a pack file

  - {term: latex_source, canonical: "LaTeX source", theme_kind: format, surfaces: [tex, latex]}

Section page ›

Dictionary word

levene

levene · Core, statistics

Kind: statistic
Spelled: levene, bartlett

As YAML for a pack file

  - {term: levene, theme_kind: statistic, surfaces: [levene, bartlett]}

Section page ›

Dictionary word

licence

licence · Core, file roles

Kind: file role
Spelled: license, licence, copying, copyright, notice

As YAML for a pack file

  - {term: licence, theme_kind: file_role, surfaces: [license, licence, copying, copyright,
     notice]}

Section page ›

Dictionary word

limit of detection

limit_of_detection · Core, statistics

Kind: statistic
Spelled: lod, loq, limit-of-detection

As YAML for a pack file

  - {term: limit_of_detection, theme_kind: statistic, surfaces: [lod, loq,
     "limit-of-detection"]}

Section page ›

Dictionary word

linear

linear · Core, statistics

Kind: statistic
Spelled: linear, lin

As YAML for a pack file

  - {term: linear, theme_kind: statistic, surfaces: [linear, lin]}

Section page ›

Dictionary word

linux metadata

linux_metadata · Core, filesystem noise

Kind: quality
Spelled: .directory, .Trash-1000, lost+found

As YAML for a pack file

  - {term: linux_metadata, theme_kind: quality, surfaces: [".directory", ".Trash-1000",
     "lost+found"], strength: decisive}

Section page ›

Dictionary word

litre

litre · Core, units

Kind: unit
Spelled: L, l, litre, litres, liter, liters

As YAML for a pack file

  - {term: litre, theme_kind: unit, surfaces: [L, l, litre, litres, liter, liters],
     dimension: volume, base: litre, factor: 1.0, ucum: L}

Section page ›

Dictionary word

lock file

lock_file · Core, formats

Kind: format
Spelled: lck, lock

As YAML for a pack file

  - {term: lock_file, canonical: "lock file", theme_kind: format, surfaces: [lck, lock],
     extension_only: [lock]}

Section page ›

Dictionary word

log

log · Core, process

Kind: process
Spelled: log, logs, logfile, stdout, stderr, trace, journal

As YAML for a pack file

  - {term: log, theme_kind: process, surfaces: [log, logs, logfile, stdout, stderr, trace,
     journal]}

Section page ›

Dictionary word

log file

log_file · Core, formats

Kind: format
Spelled: log

As YAML for a pack file

  - {term: log_file, canonical: "log file", theme_kind: format, surfaces: [log],
     extension_only: [log]}

Section page ›

Dictionary word

logarithm

logarithm · Core, statistics

Kind: statistic
Spelled: log, ln, log2, log10, logged

As YAML for a pack file

  - {term: logarithm, theme_kind: statistic, surfaces: [log, ln, log2, log10, logged]}

Section page ›

Dictionary word

logistic

logistic · Core, statistics

Kind: statistic
Spelled: logistic, sigmoid, hill, dose-response, ic50, ec50

As YAML for a pack file

  - {term: logistic, theme_kind: statistic, surfaces: [logistic, sigmoid, hill, "dose-response",
     ic50, ec50]}

Section page ›

Dictionary word

lookup table

lookup_table · Core, formats

Kind: format
Spelled: lut

As YAML for a pack file

  - {term: lookup_table, canonical: "lookup table", theme_kind: format, surfaces: [lut],
     extension_only: [lut]}

Section page ›

Dictionary word

lux

lux · Core, units

Kind: unit
Spelled: lx, lux

As YAML for a pack file

  - {term: lux, theme_kind: unit, surfaces: [lx, lux], dimension: illuminance, base: lux,
     factor: 1.0, ucum: lx}

Section page ›

Dictionary word

macos metadata

macos_metadata · Core, filesystem noise

Kind: quality
Spelled: .DS_Store, ._, __MACOSX, .Spotlight-V100, .fseventsd, .TemporaryItems, Icon\r, .apdisk

As YAML for a pack file

  - {term: macos_metadata, theme_kind: quality, surfaces: [".DS_Store", "._", __MACOSX,
     ".Spotlight-V100", ".fseventsd", ".TemporaryItems", "Icon\r", ".apdisk"], strength: decisive}

Section page ›

Dictionary word

magnification

magnification · Core, units

Kind: unit
Spelled: x, X
Ambiguous: Yes. Also read as fold

As YAML for a pack file

  - {term: magnification, theme_kind: unit, surfaces: [x, X], dimension: magnification,
     base: magnification, factor: 1.0, ambiguous_with: [fold]}

Section page ›

Dictionary word

manifest

manifest · Core, process

Kind: process
Spelled: manifest, index, inventory, listing, catalog, catalogue

As YAML for a pack file

  - {term: manifest, theme_kind: process, surfaces: [manifest, index, inventory, listing,
     catalog, catalogue]}

Section page ›

Dictionary word

manipulator

manipulator · Core, instruments

Kind: instrument
Spelled: manipulator, micromanipulator, injector, puller

As YAML for a pack file

  - {term: manipulator, theme_kind: instrument, surfaces: [manipulator, micromanipulator,
     injector, puller]}

Section page ›

Dictionary word

mann whitney

mann_whitney · Core, statistics

Kind: statistic
Spelled: mannwhitney, mann-whitney, wilcoxon, ranksum, signedrank

As YAML for a pack file

  - {term: mann_whitney, theme_kind: statistic, surfaces: [mannwhitney, "mann-whitney", wilcoxon,
     ranksum, signedrank]}

Section page ›

Dictionary word

march

march · Core, time and versions

Kind: date
Canonical: 03
Spelled: mar, march

As YAML for a pack file

  - {term: march, canonical: "03", theme_kind: date, surfaces: [mar, march]}

Section page ›

Dictionary word

markdown

markdown · Core, formats

Kind: format
Spelled: md, markdown, mdown
Ambiguous: Yes. Also read as molecular dynamics

As YAML for a pack file

  - {term: markdown, theme_kind: format, surfaces: [md, markdown, mdown],
     ambiguous_with: [molecular_dynamics], extension_only: [md]}

Section page ›

Dictionary word

marked good

good · Core, quality marks

Kind: quality
Spelled: good

As YAML for a pack file

  - {term: good, canonical: "marked good", theme_kind: quality, surfaces: [good], mark: good,
     negated_by: [not, "no"]}

Section page ›

Dictionary word

marked unwell

looks_unwell · Core, quality marks

Kind: quality
Spelled: sick, unhealthy, unwell

As YAML for a pack file

  - {term: looks_unwell, canonical: "marked unwell", theme_kind: quality, surfaces: [sick,
     unhealthy, unwell], mark: poor, negated_by: [not, "no"]}

Section page ›

Dictionary word

markup

markup_document · Core, formats

Kind: format
Spelled: html, htm, xhtml

As YAML for a pack file

  - {term: markup_document, canonical: markup, theme_kind: format, surfaces: [html, htm, xhtml]}

Section page ›

Dictionary word

masked

masked · Core, process

Kind: stage
Spelled: mask, masks, masked, masking

As YAML for a pack file

  - {term: masked, theme_kind: stage, surfaces: [mask, masks, masked, masking]}

Section page ›

Dictionary word

mass spectrometer

mass_spectrometer · Core, instruments

Kind: instrument
Spelled: massspec, mass-spec, spectrometer, ms_instrument

As YAML for a pack file

  - {term: mass_spectrometer, theme_kind: instrument, surfaces: [massspec, "mass-spec",
     spectrometer, ms_instrument]}

Section page ›

Dictionary word

MATLAB source

matlab_source · Core, formats

Kind: format
Spelled: m

As YAML for a pack file

  - {term: matlab_source, canonical: "MATLAB source", theme_kind: format, surfaces: [m],
     extension_only: [m], program: true}

Section page ›

Dictionary word

maximum

maximum · Core, statistics

Kind: statistic
Spelled: max, maximum, highest, peak

As YAML for a pack file

  - {term: maximum, theme_kind: statistic, surfaces: [max, maximum, highest, peak]}

Section page ›

Dictionary word

may

may · Core, time and versions

Kind: date
Canonical: 05
Spelled: may

As YAML for a pack file

  - {term: may, canonical: "05", theme_kind: date, surfaces: [may]}

Section page ›

Dictionary word

mean

mean · Core, statistics

Kind: statistic
Spelled: mean, avg, ave, average, mu

As YAML for a pack file

  - {term: mean, theme_kind: statistic, surfaces: [mean, avg, ave, average, mu]}

Section page ›

Dictionary word

mebibyte

mebibyte · Core, units

Kind: unit
Spelled: MiB, mebibyte

As YAML for a pack file

  - {term: mebibyte, theme_kind: unit, surfaces: [MiB, mebibyte], dimension: digital_size,
     base: byte, factor: 1048576.0, ucum: MiBy}

Section page ›

Dictionary word

median

median · Core, statistics

Kind: statistic
Spelled: median, med, p50

As YAML for a pack file

  - {term: median, theme_kind: statistic, surfaces: [median, med, p50]}

Section page ›

Dictionary word

megabyte

megabyte · Core, units

Kind: unit
Spelled: MB, megabyte

As YAML for a pack file

  - {term: megabyte, theme_kind: unit, surfaces: [MB, megabyte], dimension: digital_size,
     base: byte, factor: "1.0e6", ucum: MBy}

Section page ›

Dictionary word

megadalton

megadalton · Core, units

Kind: unit
Spelled: MDa, megadalton

As YAML for a pack file

  - {term: megadalton, theme_kind: unit, surfaces: [MDa, megadalton], dimension: molecular_mass,
     base: dalton, factor: "1.0e6", ucum: Mu}

Section page ›

Dictionary word

megaelectronvolt

megaelectronvolt · Core, units

Kind: unit
Spelled: MeV

As YAML for a pack file

  - {term: megaelectronvolt, theme_kind: unit, surfaces: [MeV], dimension: energy, base: joule,
     factor: 1.602176634e-13, ucum: MeV}

Section page ›

Dictionary word

megahertz

megahertz · Core, units

Kind: unit
Spelled: MHz, megahertz

As YAML for a pack file

  - {term: megahertz, theme_kind: unit, surfaces: [MHz, megahertz], dimension: frequency,
     base: hertz, factor: "1.0e6", ucum: MHz}

Section page ›

Dictionary word

megaohm

megaohm · Core, units

Kind: unit
Spelled: Mohm, MΩ, megaohm

As YAML for a pack file

  - {term: megaohm, theme_kind: unit, surfaces: [Mohm, "MΩ", megaohm], dimension: resistance,
     base: ohm, factor: "1.0e6", ucum: MOhm}

Section page ›

Dictionary word

megapascal

megapascal · Core, units

Kind: unit
Spelled: MPa, megapascal

As YAML for a pack file

  - {term: megapascal, theme_kind: unit, surfaces: [MPa, megapascal], dimension: pressure,
     base: pascal, factor: "1.0e6", ucum: MPa}

Section page ›

Dictionary word

merged

merged · Core, process

Kind: stage
Spelled: merge, merged, combined, joined, concatenated, concat
Ambiguous: Yes. Also read as pooled

As YAML for a pack file

  - {term: merged, theme_kind: stage, surfaces: [merge, merged, combined, joined, concatenated,
     concat], ambiguous_with: [pooled]}

Section page ›

Dictionary word

metadata

metadata · Core, file roles

Kind: file role
Spelled: metadata, meta, header, headers, sidecar, descriptor, provenance

As YAML for a pack file

  - {term: metadata, theme_kind: file_role, surfaces: [metadata, meta, header, headers, sidecar,
     descriptor, provenance]}

Section page ›

Dictionary word

metre

metre · Core, units

Kind: unit
Spelled: m, metre, metres, meter, meters

As YAML for a pack file

  - {term: metre, theme_kind: unit, surfaces: [m, metre, metres, meter, meters],
     dimension: length, base: metre, factor: 1.0, ucum: m}

Section page ›

Dictionary word

microampere

microampere · Core, units

Kind: unit
Spelled: uA, µA, μA, microamp

As YAML for a pack file

  - {term: microampere, theme_kind: unit, surfaces: [uA, "µA", "μA", microamp],
     dimension: current, base: ampere, factor: 1.0e-06, ucum: uA}

Section page ›

Dictionary word

microgram

microgram · Core, units

Kind: unit
Spelled: ug, µg, μg, mcg, microgram, micrograms

As YAML for a pack file

  - {term: microgram, theme_kind: unit, surfaces: [ug, "µg", "μg", mcg, microgram, micrograms],
     dimension: mass, base: gram, factor: 1.0e-06, ucum: ug}

Section page ›

Dictionary word

microgram per microlitre

microgram_per_microlitre · Core, units

Kind: unit
Spelled: ug/uL, µg/µL, ugul

As YAML for a pack file

  - {term: microgram_per_microlitre, theme_kind: unit, surfaces: ["ug/uL", "µg/µL", ugul],
     dimension: mass_concentration, base: gram_per_litre, factor: 1.0, ucum: "ug/uL"}

Section page ›

Dictionary word

microgram per millilitre

microgram_per_millilitre · Core, units

Kind: unit
Spelled: ug/mL, µg/mL, μg/mL, ugml, ugperml

As YAML for a pack file

  - {term: microgram_per_millilitre, theme_kind: unit, surfaces: ["ug/mL", "µg/mL", "μg/mL",
     ugml, ugperml], dimension: mass_concentration, base: gram_per_litre, factor: 0.001,
     ucum: "ug/mL"}

Section page ›

Dictionary word

microlitre

microlitre · Core, units

Kind: unit
Spelled: uL, ul, µL, µl, μL, microlitre, microliter

As YAML for a pack file

  - {term: microlitre, theme_kind: unit, surfaces: [uL, ul, "µL", "µl", "μL", microlitre,
     microliter], dimension: volume, base: litre, factor: 1.0e-06, ucum: uL}

Section page ›

Dictionary word

micrometre

micrometre · Core, units

Kind: unit
Spelled: um, µm, μm, micron, microns, micrometre, micrometer

As YAML for a pack file

  - {term: micrometre, theme_kind: unit, surfaces: [um, "µm", "μm", micron, microns, micrometre,
     micrometer], dimension: length, base: metre, factor: 1.0e-06, ucum: um}

Section page ›

Dictionary word

micromolar

micromolar · Core, units

Kind: unit
Spelled: uM, µM, μM, micromolar, umol/L

As YAML for a pack file

  - {term: micromolar, theme_kind: unit, surfaces: [uM, "µM", "μM", micromolar, "umol/L"],
     dimension: concentration, base: molar, factor: 1.0e-06, ucum: "umol/L"}

Section page ›

Dictionary word

micromole

micromole · Core, units

Kind: unit
Spelled: umol, µmol, μmol, micromole

As YAML for a pack file

  - {term: micromole, theme_kind: unit, surfaces: [umol, "µmol", "μmol", micromole],
     dimension: amount, base: mole, factor: 1.0e-06, ucum: umol}

Section page ›

Dictionary word

microscope

microscope · Core, instruments

Kind: instrument
Spelled: microscope, scope, micro, imaging_system

As YAML for a pack file

  - {term: microscope, theme_kind: instrument, surfaces: [microscope, scope, micro,
     imaging_system]}

Section page ›

Dictionary word

microsecond

microsecond · Core, units

Kind: unit
Spelled: us, µs, μs, usec, microsecond

As YAML for a pack file

  - {term: microsecond, theme_kind: unit, surfaces: [us, "µs", "μs", usec, microsecond],
     dimension: time, base: second, factor: 1.0e-06, ucum: us}

Section page ›

Dictionary word

microvolt

microvolt · Core, units

Kind: unit
Spelled: uV, µV, μV, microvolt

As YAML for a pack file

  - {term: microvolt, theme_kind: unit, surfaces: [uV, "µV", "μV", microvolt],
     dimension: voltage, base: volt, factor: 1.0e-06, ucum: uV}

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Dictionary word

microwatt

microwatt · Core, units

Kind: unit
Spelled: uW, µW, μW, microwatt

As YAML for a pack file

  - {term: microwatt, theme_kind: unit, surfaces: [uW, "µW", "μW", microwatt], dimension: power,
     base: watt, factor: 1.0e-06, ucum: uW}

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Dictionary word

milliampere

milliampere · Core, units

Kind: unit
Spelled: mA, milliamp

As YAML for a pack file

  - {term: milliampere, theme_kind: unit, surfaces: [mA, milliamp], dimension: current,
     base: ampere, factor: 0.001, ucum: mA}

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Dictionary word

millibar

millibar · Core, units

Kind: unit
Spelled: mbar, millibar

As YAML for a pack file

  - {term: millibar, theme_kind: unit, surfaces: [mbar, millibar], dimension: pressure,
     base: pascal, factor: 100.0, ucum: mbar}

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Dictionary word

milligram

milligram · Core, units

Kind: unit
Spelled: mg, milligram, milligrams

As YAML for a pack file

  - {term: milligram, theme_kind: unit, surfaces: [mg, milligram, milligrams], dimension: mass,
     base: gram, factor: 0.001, ucum: mg}

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Dictionary word

milligram per millilitre

milligram_per_millilitre · Core, units

Kind: unit
Spelled: mg/mL, mg/ml, mgml, mgpermL

As YAML for a pack file

  - {term: milligram_per_millilitre, theme_kind: unit, surfaces: ["mg/mL", "mg/ml", mgml,
     mgpermL], dimension: mass_concentration, base: gram_per_litre, factor: 1.0, ucum: "mg/mL"}

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Dictionary word

millilitre

millilitre · Core, units

Kind: unit
Spelled: mL, ml, millilitre, milliliter, cc

As YAML for a pack file

  - {term: millilitre, theme_kind: unit, surfaces: [mL, ml, millilitre, milliliter, cc],
     dimension: volume, base: litre, factor: 0.001, ucum: mL}

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Dictionary word

millimetre

millimetre · Core, units

Kind: unit
Spelled: mm, millimetre, millimeter

As YAML for a pack file

  - {term: millimetre, theme_kind: unit, surfaces: [mm, millimetre, millimeter],
     dimension: length, base: metre, factor: 0.001, ucum: mm}

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Dictionary word

millimolar

millimolar · Core, units

Kind: unit
Spelled: mM, millimolar, mmol/L

As YAML for a pack file

  - {term: millimolar, theme_kind: unit, surfaces: [mM, millimolar, "mmol/L"],
     dimension: concentration, base: molar, factor: 0.001, ucum: "mmol/L"}

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Dictionary word

millimole

millimole · Core, units

Kind: unit
Spelled: mmol, millimole

As YAML for a pack file

  - {term: millimole, theme_kind: unit, surfaces: [mmol, millimole], dimension: amount,
     base: mole, factor: 0.001, ucum: mmol}

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Dictionary word

millisecond

millisecond · Core, units

Kind: unit
Spelled: ms, msec, millisecond, milliseconds

As YAML for a pack file

  - {term: millisecond, theme_kind: unit, surfaces: [ms, msec, millisecond, milliseconds],
     dimension: time, base: second, factor: 0.001, ucum: ms}

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Dictionary word

millivolt

millivolt · Core, units

Kind: unit
Spelled: mV, millivolt

As YAML for a pack file

  - {term: millivolt, theme_kind: unit, surfaces: [mV, millivolt], dimension: voltage,
     base: volt, factor: 0.001, ucum: mV}

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Dictionary word

milliwatt

milliwatt · Core, units

Kind: unit
Spelled: mW, milliwatt

As YAML for a pack file

  - {term: milliwatt, theme_kind: unit, surfaces: [mW, milliwatt], dimension: power, base: watt,
     factor: 0.001, ucum: mW}

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Dictionary word

minimum

minimum · Core, statistics

Kind: statistic
Spelled: min, minimum, lowest

As YAML for a pack file

  - {term: minimum, theme_kind: statistic, surfaces: [min, minimum, lowest]}

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Dictionary word

minute

minute · Core, units

Kind: unit
Spelled: min, mins, minute, minutes

As YAML for a pack file

  - {term: minute, theme_kind: unit, surfaces: [min, mins, minute, minutes], dimension: time,
     base: second, factor: 60.0, ucum: min}

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Dictionary word

mode

mode · Core, statistics

Kind: statistic
Spelled: mode

As YAML for a pack file

  - {term: mode, theme_kind: statistic, surfaces: [mode]}

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Dictionary word

molar

molar · Core, units

Kind: unit
Spelled: M, molar, mol/L, mol/l

As YAML for a pack file

  - {term: molar, theme_kind: unit, surfaces: [M, molar, "mol/L", "mol/l"],
     dimension: concentration, base: molar, factor: 1.0, ucum: "mol/L"}

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Dictionary word

mole

mole · Core, units

Kind: unit
Spelled: mol, mole, moles

As YAML for a pack file

  - {term: mole, theme_kind: unit, surfaces: [mol, mole, moles], dimension: amount, base: mole,
     factor: 1.0, ucum: mol}

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Dictionary word

monday

monday · Core, time and versions

Kind: date
Spelled: monday

As YAML for a pack file

  - {term: monday, theme_kind: date, surfaces: [monday], weekday: 1, stamp_abbreviation: mon}

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Dictionary word

month

month · Core, units

Kind: unit
Spelled: mo, month, months

As YAML for a pack file

  - {term: month, theme_kind: unit, surfaces: [mo, month, months], dimension: time, base: second,
     factor: 2629800.0, ucum: mo}

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Dictionary word

morning

morning · Core, time and versions

Kind: date
Spelled: am, morning

As YAML for a pack file

  - {term: morning, theme_kind: date, surfaces: [am, morning]}

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Dictionary word

movie

movie · Core, file roles

Kind: file role
Spelled: movie, movies, video, videos, clip, animation

As YAML for a pack file

  - {term: movie, theme_kind: file_role, surfaces: [movie, movies, video, videos, clip,
     animation]}

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Dictionary word

nanoampere

nanoampere · Core, units

Kind: unit
Spelled: nA, nanoamp

As YAML for a pack file

  - {term: nanoampere, theme_kind: unit, surfaces: [nA, nanoamp], dimension: current,
     base: ampere, factor: 1.0e-09, ucum: nA}

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Dictionary word

nanogram

nanogram · Core, units

Kind: unit
Spelled: ng, nanogram, nanograms

As YAML for a pack file

  - {term: nanogram, theme_kind: unit, surfaces: [ng, nanogram, nanograms], dimension: mass,
     base: gram, factor: 1.0e-09, ucum: ng}

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Dictionary word

nanogram per millilitre

nanogram_per_millilitre · Core, units

Kind: unit
Spelled: ng/mL, ng/ml, ngml, ngperml

As YAML for a pack file

  - {term: nanogram_per_millilitre, theme_kind: unit, surfaces: ["ng/mL", "ng/ml", ngml,
     ngperml], dimension: mass_concentration, base: gram_per_litre, factor: 1.0e-06, ucum: "ng/mL"}

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Dictionary word

nanolitre

nanolitre · Core, units

Kind: unit
Spelled: nL, nl, nanolitre, nanoliter

As YAML for a pack file

  - {term: nanolitre, theme_kind: unit, surfaces: [nL, nl, nanolitre, nanoliter],
     dimension: volume, base: litre, factor: 1.0e-09, ucum: nL}

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Dictionary word

nanometre

nanometre · Core, units

Kind: unit
Spelled: nm, nanometre, nanometer

As YAML for a pack file

  - {term: nanometre, theme_kind: unit, surfaces: [nm, nanometre, nanometer], dimension: length,
     base: metre, factor: 1.0e-09, ucum: nm}

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Dictionary word

nanomolar

nanomolar · Core, units

Kind: unit
Spelled: nM, nanomolar, nmol/L

As YAML for a pack file

  - {term: nanomolar, theme_kind: unit, surfaces: [nM, nanomolar, "nmol/L"],
     dimension: concentration, base: molar, factor: 1.0e-09, ucum: "nmol/L"}

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Dictionary word

nanomole

nanomole · Core, units

Kind: unit
Spelled: nmol, nanomole

As YAML for a pack file

  - {term: nanomole, theme_kind: unit, surfaces: [nmol, nanomole], dimension: amount, base: mole,
     factor: 1.0e-09, ucum: nmol}

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Dictionary word

nanosecond

nanosecond · Core, units

Kind: unit
Spelled: ns, nsec, nanosecond

As YAML for a pack file

  - {term: nanosecond, theme_kind: unit, surfaces: [ns, nsec, nanosecond], dimension: time,
     base: second, factor: 1.0e-09, ucum: ns}

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Dictionary word

nanosiemens

nanosiemens · Core, units

Kind: unit
Spelled: nS, nanosiemens

As YAML for a pack file

  - {term: nanosiemens, theme_kind: unit, surfaces: [nS, nanosiemens], dimension: conductance,
     base: siemens, factor: 1.0e-09, ucum: nS}

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Dictionary word

new folder

new_folder · Core, negative lexicon

Kind: quality
Spelled: newfolder, new folder, new-folder, untitledfolder, folder1, foldera

As YAML for a pack file

  - {term: new_folder, theme_kind: quality, surfaces: [newfolder, "new folder", "new-folder",
     untitledfolder, folder1, foldera], strength: strong}

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Dictionary word

noise

noise · Core, statistics

Kind: statistic
Spelled: noise, background, bg, blank, dark

As YAML for a pack file

  - {term: noise, theme_kind: statistic, surfaces: [noise, background, bg, blank, dark]}

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Dictionary word

nonlinear

nonlinear · Core, statistics

Kind: statistic
Spelled: nonlinear, non-linear, nls

As YAML for a pack file

  - {term: nonlinear, theme_kind: statistic, surfaces: [nonlinear, "non-linear", nls]}

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Dictionary word

normalised

normalised · Core, process

Kind: stage
Spelled: norm, normalised, normalized, normalisation, normalization

As YAML for a pack file

  - {term: normalised, theme_kind: stage, surfaces: [norm, normalised, normalized, normalisation,
     normalization]}

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Dictionary word

notebook

notebook · Core, process

Kind: process
Spelled: notebook, notebooks, nb

As YAML for a pack file

  - {term: notebook, theme_kind: process, surfaces: [notebook, notebooks, nb]}

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Dictionary word

notebook

notebook_format · Core, formats

Kind: format
Spelled: ipynb

As YAML for a pack file

  - {term: notebook_format, canonical: notebook, theme_kind: format, surfaces: [ipynb],
     program: true}

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Dictionary word

notes

notes · Core, file roles

Kind: file role
Spelled: notes, note, memo, comments, remarks, observations, journal_notes, labnotes and 1 more

As YAML for a pack file

  - {term: notes, theme_kind: file_role, surfaces: [notes, note, memo, comments, remarks,
     observations, journal_notes, labnotes, "lab-notes"]}

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Dictionary word

november

november · Core, time and versions

Kind: date
Canonical: 11
Spelled: nov, november

As YAML for a pack file

  - {term: november, canonical: "11", theme_kind: date, surfaces: [nov, november]}

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Dictionary word

numerical aperture

numerical_aperture · Core, units

Kind: unit
Spelled: NA

As YAML for a pack file

  - {term: numerical_aperture, theme_kind: unit, surfaces: [NA], dimension: numerical_aperture,
     base: numerical_aperture, factor: 1.0}

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Dictionary word

objective

objective · Core, instruments

Kind: instrument
Spelled: objective, obj, lens, lenses

As YAML for a pack file

  - {term: objective, theme_kind: instrument, surfaces: [objective, obj, lens, lenses]}

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Dictionary word

obsolete

obsolete · Core, negative lexicon

Kind: quality
Spelled: obsolete, outdated, stale, expired, legacy, oldversion

As YAML for a pack file

  - {term: obsolete, theme_kind: quality, surfaces: [obsolete, outdated, stale, expired, legacy,
     oldversion], strength: strong}

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Dictionary word

october

october · Core, time and versions

Kind: date
Canonical: 10
Spelled: oct, october

As YAML for a pack file

  - {term: october, canonical: "10", theme_kind: date, surfaces: [oct, october]}

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Dictionary word

of

of · Core, connecting words

Kind: connective
Spelled: of

As YAML for a pack file

  - {term: of, theme_kind: connective, surfaces: [of]}

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Dictionary word

ohm

ohm · Core, units

Kind: unit
Spelled: ohm, ohms, Ω

As YAML for a pack file

  - {term: ohm, theme_kind: unit, surfaces: [ohm, ohms, "Ω"], dimension: resistance, base: ohm,
     factor: 1.0, ucum: Ohm}

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Dictionary word

or

or · Core, connecting words

Kind: connective
Spelled: or

As YAML for a pack file

  - {term: or, theme_kind: connective, surfaces: [or]}

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Dictionary word

original

original · Core, time and versions

Kind: version
Spelled: original, source, master

As YAML for a pack file

  - {term: original, theme_kind: version, surfaces: [original, source, master]}

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Dictionary word

original kept aside

kept_original · Core, time and versions

Kind: version
Spelled: orig

As YAML for a pack file

  - {term: kept_original, canonical: "original kept aside", theme_kind: version,
     surfaces: [orig]}

Section page ›

Dictionary word

overnight

overnight · Core, time and versions

Kind: date
Spelled: overnight, o/n, ovn

As YAML for a pack file

  - {term: overnight, theme_kind: date, surfaces: [overnight, "o/n", ovn]}

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Dictionary word

p value

p_value · Core, statistics

Kind: statistic
Spelled: p, pval, pvalue, p-value, pvals

As YAML for a pack file

  - {term: p_value, theme_kind: statistic, surfaces: [p, pval, pvalue, "p-value", pvals]}

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Dictionary word

package relationship part

package_relationship_part · Core, formats

Kind: format
Spelled: rels

As YAML for a pack file

  - {term: package_relationship_part, canonical: "package relationship part", theme_kind: format,
     surfaces: [rels]}

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Dictionary word

partial

partial · Core, process

Kind: status
Spelled: partial, incomplete, truncated, unfinished

As YAML for a pack file

  - {term: partial, theme_kind: status, surfaces: [partial, incomplete, truncated, unfinished]}

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Dictionary word

parts per billion

parts_per_billion · Core, units

Kind: unit
Spelled: ppb

As YAML for a pack file

  - {term: parts_per_billion, theme_kind: unit, surfaces: [ppb], dimension: fraction,
     base: fraction, factor: 1.0e-09, ucum: "[ppb]"}

Section page ›

Dictionary word

parts per million

parts_per_million · Core, units

Kind: unit
Spelled: ppm

As YAML for a pack file

  - {term: parts_per_million, theme_kind: unit, surfaces: [ppm], dimension: fraction,
     base: fraction, factor: 1.0e-06, ucum: "[ppm]"}

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Dictionary word

pascal

pascal · Core, units

Kind: unit
Spelled: Pa, pascal

As YAML for a pack file

  - {term: pascal, theme_kind: unit, surfaces: [Pa, pascal], dimension: pressure, base: pascal,
     factor: 1.0, ucum: Pa}

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Dictionary word

PDF

portable_document · Core, formats

Kind: format
Spelled: pdf

As YAML for a pack file

  - {term: portable_document, canonical: PDF, theme_kind: format, surfaces: [pdf]}

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Dictionary word

pending

pending · Core, process

Kind: status
Spelled: pending, queued, waiting, todo, scheduled

As YAML for a pack file

  - {term: pending, theme_kind: status, surfaces: [pending, queued, waiting, todo, scheduled]}

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Dictionary word

per

per · Core, connecting words

Kind: connective
Spelled: per

As YAML for a pack file

  - {term: per, theme_kind: connective, surfaces: [per]}

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Dictionary word

percent

percent · Core, units

Kind: unit
Spelled: %, pct, percent

As YAML for a pack file

  - {term: percent, theme_kind: unit, surfaces: ["%", pct, percent], dimension: fraction,
     base: fraction, factor: 0.01, ucum: "%"}

Section page ›

Dictionary word

percent change

percent_change · Core, statistics

Kind: statistic
Spelled: pctchange, percent-change, relchange

As YAML for a pack file

  - {term: percent_change, theme_kind: statistic, surfaces: [pctchange, "percent-change",
     relchange]}

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Dictionary word

percent volume volume

percent_volume_volume · Core, units

Kind: unit
Spelled: %v/v, vv, v/v

As YAML for a pack file

  - {term: percent_volume_volume, theme_kind: unit, surfaces: ["%v/v", vv, "v/v"],
     dimension: fraction, base: fraction, factor: 0.01}

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Dictionary word

percent weight volume

percent_weight_volume · Core, units

Kind: unit
Spelled: %w/v, wv, w/v

As YAML for a pack file

  - {term: percent_weight_volume, theme_kind: unit, surfaces: ["%w/v", wv, "w/v"],
     dimension: fraction, base: fraction, factor: 0.01}

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Dictionary word

percentile

percentile · Core, statistics

Kind: statistic
Spelled: pct, percentile, quantile, p95, p99

As YAML for a pack file

  - {term: percentile, theme_kind: statistic, surfaces: [pct, percentile, quantile, p95, p99]}

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Dictionary word

Perl

perl_source · Core, formats

Kind: format
Spelled: pl, pm

As YAML for a pack file

  - {term: perl_source, canonical: Perl, theme_kind: format, surfaces: [pl, pm],
     extension_only: [pl, pm], program: true}

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Dictionary word

petabyte

petabyte · Core, units

Kind: unit
Spelled: PB, petabyte

As YAML for a pack file

  - {term: petabyte, theme_kind: unit, surfaces: [PB, petabyte], dimension: digital_size,
     base: byte, factor: "1.0e15", ucum: PBy}

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Dictionary word

ph meter

ph_meter · Core, instruments

Kind: instrument
Spelled: phmeter, ph-meter, probe_ph

As YAML for a pack file

  - {term: ph_meter, theme_kind: instrument, surfaces: [phmeter, "ph-meter", probe_ph]}

Section page ›

Dictionary word

picoampere

picoampere · Core, units

Kind: unit
Spelled: pA, picoamp

As YAML for a pack file

  - {term: picoampere, theme_kind: unit, surfaces: [pA, picoamp], dimension: current,
     base: ampere, factor: 1.0e-12, ucum: pA}

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Dictionary word

picofarad

picofarad · Core, units

Kind: unit
Spelled: pF, picofarad

As YAML for a pack file

  - {term: picofarad, theme_kind: unit, surfaces: [pF, picofarad], dimension: capacitance,
     base: farad, factor: 1.0e-12, ucum: pF}

Section page ›

Dictionary word

picogram

picogram · Core, units

Kind: unit
Spelled: pg, picogram, picograms

As YAML for a pack file

  - {term: picogram, theme_kind: unit, surfaces: [pg, picogram, picograms], dimension: mass,
     base: gram, factor: 1.0e-12, ucum: pg}

Section page ›

Dictionary word

picolitre

picolitre · Core, units

Kind: unit
Spelled: pL, pl, picolitre, picoliter

As YAML for a pack file

  - {term: picolitre, theme_kind: unit, surfaces: [pL, pl, picolitre, picoliter],
     dimension: volume, base: litre, factor: 1.0e-12, ucum: pL}

Section page ›

Dictionary word

picometre

picometre · Core, units

Kind: unit
Spelled: pm, picometre, picometer

As YAML for a pack file

  - {term: picometre, theme_kind: unit, surfaces: [pm, picometre, picometer], dimension: length,
     base: metre, factor: 1.0e-12, ucum: pm}

Section page ›

Dictionary word

picomolar

picomolar · Core, units

Kind: unit
Spelled: pM, picomolar, pmol/L

As YAML for a pack file

  - {term: picomolar, theme_kind: unit, surfaces: [pM, picomolar, "pmol/L"],
     dimension: concentration, base: molar, factor: 1.0e-12, ucum: "pmol/L"}

Section page ›

Dictionary word

picomole

picomole · Core, units

Kind: unit
Spelled: pmol, picomole

As YAML for a pack file

  - {term: picomole, theme_kind: unit, surfaces: [pmol, picomole], dimension: amount, base: mole,
     factor: 1.0e-12, ucum: pmol}

Section page ›

Dictionary word

pipeline

pipeline · Core, process

Kind: process
Spelled: pipeline, workflow, flow, dag

As YAML for a pack file

  - {term: pipeline, theme_kind: process, surfaces: [pipeline, workflow, flow, dag]}

Section page ›

Dictionary word

pixel

pixel · Core, units

Kind: unit
Spelled: px, pixel, pixels

As YAML for a pack file

  - {term: pixel, theme_kind: unit, surfaces: [px, pixel, pixels], dimension: pixels,
     base: pixel, factor: 1.0}

Section page ›

Dictionary word

plain text

plain_text · Core, formats

Kind: format
Spelled: txt, text

As YAML for a pack file

  - {term: plain_text, canonical: "plain text", theme_kind: format, surfaces: [txt, text]}

Section page ›

Dictionary word

plate

plate · Core, process

Kind: vessel
Spelled: plate, plates, wellplate, microplate

As YAML for a pack file

  - {term: plate, theme_kind: vessel, surfaces: [plate, plates, wellplate, microplate]}

Section page ›

Dictionary word

plate reader

plate_reader · Core, instruments

Kind: instrument
Spelled: platereader, plate-reader, reader, spectrophotometer, luminometer, fluorimeter, fluorometer

As YAML for a pack file

  - {term: plate_reader, theme_kind: instrument, surfaces: [platereader, "plate-reader", reader,
     spectrophotometer, luminometer, fluorimeter, fluorometer]}

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Dictionary word

playlist

playlist_format · Core, formats

Kind: format
Spelled: m3u, m3u8, pls

As YAML for a pack file

  - {term: playlist_format, canonical: playlist, theme_kind: format, surfaces: [m3u, m3u8, pls]}

Section page ›

Dictionary word

plot

plot · Core, file roles

Kind: file role
Spelled: plot, plots, chart, charts, graph, graphs, diagram

As YAML for a pack file

  - {term: plot, theme_kind: file_role, surfaces: [plot, plots, chart, charts, graph, graphs,
     diagram], product: true}

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Dictionary word

polynomial

polynomial · Core, statistics

Kind: statistic
Spelled: poly, polynomial, quadratic, cubic

As YAML for a pack file

  - {term: polynomial, theme_kind: statistic, surfaces: [poly, polynomial, quadratic, cubic]}

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Dictionary word

pooled

pooled · Core, process

Kind: stage
Spelled: pooled, pooling, metaanalysis, meta-analysis, meta_analysis, combined, merged, final and 1 more
Ambiguous: Yes. Also read as final, merged

As YAML for a pack file

  - {term: pooled, theme_kind: stage, surfaces: [pooled, pooling, metaanalysis, "meta-analysis",
     meta_analysis, combined, merged, final, AAA], ambiguous_with: [merged, final]}

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Dictionary word

position

position · Core, process

Kind: position
Spelled: pos, position, positions, site, sites, fov, field-of-view

As YAML for a pack file

  - {term: position, theme_kind: position, surfaces: [pos, position, positions, site, sites, fov,
     "field-of-view"]}

Section page ›

Dictionary word

pre-treatment

pretreatment · Core, process

Kind: condition
Spelled: pre, pretreatment, pre-treatment, pretreated, pre-treated

As YAML for a pack file

  - {term: pretreatment, canonical: "pre-treatment", theme_kind: condition, surfaces: [pre,
     pretreatment, "pre-treatment", pretreated, "pre-treated"]}

Section page ›

Dictionary word

precision

precision · Core, statistics

Kind: statistic
Spelled: precision, ppv

As YAML for a pack file

  - {term: precision, theme_kind: statistic, surfaces: [precision, ppv]}

Section page ›

Dictionary word

preprocessed

preprocessed · Core, process

Kind: stage
Spelled: prep, prepped, preprocessed, preprocessing, pre-processed

As YAML for a pack file

  - {term: preprocessed, theme_kind: stage, surfaces: [prep, prepped, preprocessed,
     preprocessing, "pre-processed"]}

Section page ›

Dictionary word

presentation

presentation · Core, file roles

Kind: file role
Spelled: presentation, slides, deck, talk, seminar, poster

As YAML for a pack file

  - {term: presentation, theme_kind: file_role, surfaces: [presentation, slides, deck, talk,
     seminar, poster], product: true}

Section page ›

Dictionary word

presentation

slide_deck_format · Core, formats

Kind: format
Spelled: pptx, ppt, odp

As YAML for a pack file

  - {term: slide_deck_format, canonical: presentation, theme_kind: format, surfaces: [pptx, ppt,
     odp], product: true}

Section page ›

Dictionary word

Kind: version
Spelled: prev, previous, prior, last

As YAML for a pack file

  - {term: previous, theme_kind: version, surfaces: [prev, previous, prior, last]}

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Dictionary word

principal component analysis

principal_component_analysis · Core, statistics

Kind: statistic
Spelled: pca, pc1, pc2, principal

As YAML for a pack file

  - {term: principal_component_analysis, theme_kind: statistic, surfaces: [pca, pc1, pc2,
     principal]}

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Dictionary word

processed

processed · Core, process

Kind: stage
Spelled: processed, processing, proc

As YAML for a pack file

  - {term: processed, theme_kind: stage, surfaces: [processed, processing, proc]}

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Dictionary word

program output

program_output · Core, formats

Kind: format
Spelled: out

As YAML for a pack file

  - {term: program_output, canonical: "program output", theme_kind: format, surfaces: [out],
     extension_only: [out]}

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Dictionary word

project

project · Core, process

Kind: project
Spelled: project, proj, programme, program

As YAML for a pack file

  - {term: project, theme_kind: project, surfaces: [project, proj, programme, program]}

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Dictionary word

projected

projected · Core, process

Kind: stage
Spelled: proj, projected, projection

As YAML for a pack file

  - {term: projected, theme_kind: stage, surfaces: [proj, projected, projection]}

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Dictionary word

protocol

protocol · Core, file roles

Kind: file role
Spelled: protocol, protocols, sop, procedure, method, methods, recipe, instructions

As YAML for a pack file

  - {term: protocol, theme_kind: file_role, surfaces: [protocol, protocols, sop, procedure,
     method, methods, recipe, instructions]}

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Dictionary word

psi

psi · Core, units

Kind: unit
Spelled: psi

As YAML for a pack file

  - {term: psi, theme_kind: unit, surfaces: [psi], dimension: pressure, base: pascal,
     factor: 6894.757, ucum: "[psi]"}

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Dictionary word

Python bytecode

python_bytecode · Core, formats

Kind: format
Spelled: pyc, pyo

As YAML for a pack file

  - {term: python_bytecode, canonical: "Python bytecode", theme_kind: format, surfaces: [pyc,
     pyo], program: true}

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Dictionary word

Python source

python_source · Core, formats

Kind: format
Spelled: py, pyi, pyx

As YAML for a pack file

  - {term: python_source, canonical: "Python source", theme_kind: format, surfaces: [py, pyi,
     pyx], program: true}

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Dictionary word

quantification

quantification · Core, process

Kind: stage
Spelled: quant, quantified, quantification, measurements, measured

As YAML for a pack file

  - {term: quantification, theme_kind: stage, surfaces: [quant, quantified, quantification,
     measurements, measured]}

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Dictionary word

quarantine

quarantine · Core, negative lexicon

Kind: quality
Spelled: quarantine, quarantined, isolated, held, onhold, on-hold, parked

As YAML for a pack file

  - {term: quarantine, theme_kind: quality, surfaces: [quarantine, quarantined, isolated, held,
     onhold, "on-hold", parked], strength: low}

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Dictionary word

quartile

quartile · Core, statistics

Kind: statistic
Spelled: q1, q3, quartile, quartiles

As YAML for a pack file

  - {term: quartile, theme_kind: statistic, surfaces: [q1, q3, quartile, quartiles]}

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Dictionary word

questionable

questionable · Core, negative lexicon

Kind: quality
Spelled: questionable, suspect, suspicious, dodgy, sketchy, weird, odd, strange

As YAML for a pack file

  - {term: questionable, theme_kind: quality, surfaces: [questionable, suspect, suspicious,
     dodgy, sketchy, weird, odd, strange], strength: low}

Section page ›

Dictionary word

R Markdown

r_markdown · Core, formats

Kind: format
Spelled: rmd, rmarkdown

As YAML for a pack file

  - {term: r_markdown, canonical: "R Markdown", theme_kind: format, surfaces: [rmd, rmarkdown],
     program: true}

Section page ›

Dictionary word

R source

r_source · Core, formats

Kind: format
Spelled: r

As YAML for a pack file

  - {term: r_source, canonical: "R source", theme_kind: format, surfaces: [r],
     extension_only: [r], program: true}

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Dictionary word

r squared

r_squared · Core, statistics

Kind: statistic
Spelled: r2, rsq, rsquared, r-squared, adjr2

As YAML for a pack file

  - {term: r_squared, theme_kind: statistic, surfaces: [r2, rsq, rsquared, "r-squared", adjr2]}

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Dictionary word

R workspace

r_workspace · Core, formats

Kind: format
Spelled: rds, rdata

As YAML for a pack file

  - {term: r_workspace, canonical: "R workspace", theme_kind: format, surfaces: [rds, rdata],
     extension_only: [rdata]}

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Dictionary word

radian

radian · Core, units

Kind: unit
Spelled: rad, radian, radians

As YAML for a pack file

  - {term: radian, theme_kind: unit, surfaces: [rad, radian, radians], dimension: angle,
     base: degree, factor: 57.29577951308232, ucum: rad}

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Dictionary word

range

range · Core, statistics

Kind: statistic
Spelled: range, spread

As YAML for a pack file

  - {term: range, theme_kind: statistic, surfaces: [range, spread]}

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Dictionary word

ratio

ratio · Core, statistics

Kind: statistic
Spelled: ratio, quotient, relative

As YAML for a pack file

  - {term: ratio, theme_kind: statistic, surfaces: [ratio, quotient, relative]}

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Dictionary word

raw

raw · Core, process

Kind: stage
Spelled: raw, unprocessed, untouched, asacquired, as-acquired, original_data, rawimages, rawdata

As YAML for a pack file

  - {term: raw, theme_kind: stage, surfaces: [raw, unprocessed, untouched, asacquired,
     "as-acquired", original_data, rawimages, rawdata]}

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Dictionary word

readme

readme · Core, file roles

Kind: file role
Spelled: readme, read-me, aboutthis, about

As YAML for a pack file

  - {term: readme, theme_kind: file_role, surfaces: [readme, "read-me", aboutthis, about]}

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Dictionary word

receiver operating characteristic

receiver_operating_characteristic · Core, statistics

Kind: statistic
Spelled: roc, auroc

As YAML for a pack file

  - {term: receiver_operating_characteristic, theme_kind: statistic, surfaces: [roc, auroc]}

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Dictionary word

recovered

recovered · Core, negative lexicon

Kind: quality
Spelled: recovered, recovery, restored, salvaged, autosave, autorecover, crashrecovery

As YAML for a pack file

  - {term: recovered, theme_kind: quality, surfaces: [recovered, recovery, restored, salvaged,
     autosave, autorecover, crashrecovery], strength: moderate}

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Dictionary word

redo

redo · Core, negative lexicon

Kind: quality
Spelled: redo, redone, rerun_after_fail, repeat_of, attempt2, attempt3, secondtry, tryagain

As YAML for a pack file

  - {term: redo, theme_kind: quality, surfaces: [redo, redone, rerun_after_fail, repeat_of,
     attempt2, attempt3, secondtry, tryagain], strength: moderate}

Section page ›

Dictionary word

reference data

reference_data · Core, file roles

Kind: file role
Spelled: reference, ref, standard, standards, groundtruth, ground-truth, gt, truth and 1 more

As YAML for a pack file

  - {term: reference_data, theme_kind: file_role, surfaces: [reference, ref, standard, standards,
     groundtruth, "ground-truth", gt, truth, gold]}

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Dictionary word

reference manager library

reference_library · Core, formats

Kind: format
Spelled: enl

As YAML for a pack file

  - {term: reference_library, canonical: "reference manager library", theme_kind: format,
     surfaces: [enl]}

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Dictionary word

regression

regression · Core, statistics

Kind: statistic
Spelled: reg, regression, lm, glm, ols, mixed, lme, lmm

As YAML for a pack file

  - {term: regression, theme_kind: statistic, surfaces: [reg, regression, lm, glm, ols, mixed,
     lme, lmm]}

Section page ›

Dictionary word

relative centrifugal force

relative_centrifugal_force · Core, units

Kind: unit
Spelled: rcf, xg, x g, RCF

As YAML for a pack file

  - {term: relative_centrifugal_force, theme_kind: unit, surfaces: [rcf, xg, "x g", RCF],
     dimension: acceleration, base: rcf, factor: 1.0}

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Dictionary word

release

release · Core, time and versions

Kind: version
Spelled: rel, release

As YAML for a pack file

  - {term: release, theme_kind: version, surfaces: [rel, release]}

Section page ›

Dictionary word

replicate

replicate · Core, time and versions

Kind: replicate
Spelled: rep, reps, replicate, replicates, repeat

As YAML for a pack file

  - {term: replicate, theme_kind: replicate, surfaces: [rep, reps, replicate, replicates,
     repeat]}

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Dictionary word

report

report · Core, process

Kind: stage
Spelled: report, reports, writeup, write-up, manuscript, paper, poster, slides and 1 more

As YAML for a pack file

  - {term: report, theme_kind: stage, surfaces: [report, reports, writeup, "write-up",
     manuscript, paper, poster, slides, deck]}

Section page ›

Dictionary word

rerun

rerun · Core, time and versions

Kind: replicate
Spelled: rerun, redo, again, retry

As YAML for a pack file

  - {term: rerun, theme_kind: replicate, surfaces: [rerun, redo, again, retry]}

Section page ›

Dictionary word

residual

residual · Core, statistics

Kind: statistic
Spelled: resid, residual, residuals, error_term

As YAML for a pack file

  - {term: residual, theme_kind: statistic, surfaces: [resid, residual, residuals, error_term]}

Section page ›

Dictionary word

resized

resized · Core, process

Kind: stage
Spelled: resize, resized, rescaled, scaled

As YAML for a pack file

  - {term: resized, theme_kind: stage, surfaces: [resize, resized, rescaled, scaled]}

Section page ›

Dictionary word

reStructuredText

restructured_text · Core, formats

Kind: format
Spelled: rst

As YAML for a pack file

  - {term: restructured_text, canonical: reStructuredText, theme_kind: format, surfaces: [rst]}

Section page ›

Dictionary word

revision

revision · Core, time and versions

Kind: version
Spelled: r, rev, revision

As YAML for a pack file

  - {term: revision, theme_kind: version, surfaces: [r, rev, revision]}

Section page ›

Dictionary word

revolutions per minute

revolutions_per_minute · Core, units

Kind: unit
Spelled: rpm, RPM

As YAML for a pack file

  - {term: revolutions_per_minute, theme_kind: unit, surfaces: [rpm, RPM], dimension: rotation,
     base: rpm, factor: 1.0}

Section page ›

Dictionary word

round

round · Core, time and versions

Kind: replicate
Spelled: round, rounds, pass, passes, cycle, cycles

As YAML for a pack file

  - {term: round, theme_kind: replicate, surfaces: [round, rounds, pass, passes, cycle, cycles]}

Section page ›

Dictionary word

Ruby source

ruby_source · Core, formats

Kind: format
Spelled: rb

As YAML for a pack file

  - {term: ruby_source, canonical: "Ruby source", theme_kind: format, surfaces: [rb],
     extension_only: [rb], program: true}

Section page ›

Dictionary word

run

run · Core, process

Kind: process
Spelled: run, runs, execution, exec

As YAML for a pack file

  - {term: run, theme_kind: process, surfaces: [run, runs, execution, exec]}

Section page ›

Dictionary word

running

running · Core, process

Kind: status
Spelled: running, active, inprogress, in-progress

As YAML for a pack file

  - {term: running, theme_kind: status, surfaces: [running, active, inprogress, "in-progress"]}

Section page ›

Dictionary word

sample

sample · Core, process

Kind: sample
Spelled: sample, samples, spec, specimen, specimens

As YAML for a pack file

  - {term: sample, theme_kind: sample, surfaces: [sample, samples, spec, specimen, specimens]}

Section page ›

Dictionary word

saturday

saturday · Core, time and versions

Kind: date
Spelled: saturday

As YAML for a pack file

  - {term: saturday, theme_kind: date, surfaces: [saturday], weekday: 6,
     stamp_abbreviation: sat}

Section page ›

Dictionary word

scanner

scanner · Core, instruments

Kind: instrument
Spelled: scanner, slidescanner, gel_scanner, densitometer

As YAML for a pack file

  - {term: scanner, theme_kind: instrument, surfaces: [scanner, slidescanner, gel_scanner,
     densitometer]}

Section page ›

Dictionary word

scatter plot

scatter_plot · Core, file roles

Kind: file role
Spelled: scatter, scatterplot, scatter-plot

As YAML for a pack file

  - {term: scatter_plot, theme_kind: file_role, surfaces: [scatter, scatterplot, "scatter-plot"],
     product: true}

Section page ›

Dictionary word

schema

schema · Core, file roles

Kind: file role
Spelled: schema, schemas, spec, specification, definition, ddl

As YAML for a pack file

  - {term: schema, theme_kind: file_role, surfaces: [schema, schemas, spec, specification,
     definition, ddl]}

Section page ›

Dictionary word

scratch

scratch · Core, negative lexicon

Kind: quality
Spelled: scratch, scratchpad, sandbox, playground, workspace_tmp

As YAML for a pack file

  - {term: scratch, theme_kind: quality, surfaces: [scratch, scratchpad, sandbox, playground,
     workspace_tmp], strength: strong}

Section page ›

Dictionary word

script

script · Core, process

Kind: process
Spelled: script, scripts, macro, macros, code

As YAML for a pack file

  - {term: script, theme_kind: process, surfaces: [script, scripts, macro, macros, code]}

Section page ›

Dictionary word

second

second · Core, units

Kind: unit
Spelled: s, sec, secs, second, seconds

As YAML for a pack file

  - {term: second, theme_kind: unit, surfaces: [s, sec, secs, second, seconds], dimension: time,
     base: second, factor: 1.0, ucum: s}

Section page ›

Dictionary word

segment

segment · Core, process

Kind: part
Spelled: segment, segments

As YAML for a pack file

  - {term: segment, theme_kind: part, surfaces: [segment, segments]}

Section page ›

Dictionary word

segmented

segmented · Core, process

Kind: stage
Spelled: seg, segmented, segmentation

As YAML for a pack file

  - {term: segmented, theme_kind: stage, surfaces: [seg, segmented, segmentation]}

Section page ›

Dictionary word

sensitivity

sensitivity · Core, statistics

Kind: statistic
Spelled: sensitivity, recall, tpr

As YAML for a pack file

  - {term: sensitivity, theme_kind: statistic, surfaces: [sensitivity, recall, tpr]}

Section page ›

Dictionary word

september

september · Core, time and versions

Kind: date
Canonical: 09
Spelled: sep, sept, september

As YAML for a pack file

  - {term: september, canonical: "09", theme_kind: date, surfaces: [sep, sept, september]}

Section page ›

Dictionary word

sequencer

sequencer · Core, instruments

Kind: instrument
Spelled: sequencer, sequencing_machine, flowcell_machine

As YAML for a pack file

  - {term: sequencer, theme_kind: instrument, surfaces: [sequencer, sequencing_machine,
     flowcell_machine]}

Section page ›

Dictionary word

session

session · Core, process

Kind: session
Spelled: session, sessions, sitting

As YAML for a pack file

  - {term: session, theme_kind: session, surfaces: [session, sessions, sitting]}

Section page ›

Dictionary word

shapiro wilk

shapiro_wilk · Core, statistics

Kind: statistic
Spelled: shapiro, shapiro-wilk

As YAML for a pack file

  - {term: shapiro_wilk, theme_kind: statistic, surfaces: [shapiro, "shapiro-wilk"]}

Section page ›

Dictionary word

shell script

shell_script · Core, formats

Kind: format
Spelled: sh, bash, zsh

As YAML for a pack file

  - {term: shell_script, canonical: "shell script", theme_kind: format, surfaces: [sh, bash,
     zsh], program: true}

Section page ›

Dictionary word

siemens

siemens · Core, units

Kind: unit
Spelled: S, siemens

As YAML for a pack file

  - {term: siemens, theme_kind: unit, surfaces: [S, siemens], dimension: conductance,
     base: siemens, factor: 1.0, ucum: S}

Section page ›

Dictionary word

sievert

sievert · Core, units

Kind: unit
Spelled: Sv, sievert

As YAML for a pack file

  - {term: sievert, theme_kind: unit, surfaces: [Sv, sievert], dimension: equivalent_dose,
     base: sievert, factor: 1.0, ucum: Sv}

Section page ›

Dictionary word

signal

signal · Core, statistics

Kind: statistic
Spelled: signal, sig_intensity, amplitude

As YAML for a pack file

  - {term: signal, theme_kind: statistic, surfaces: [signal, sig_intensity, amplitude]}

Section page ›

Dictionary word

signal to noise

signal_to_noise · Core, statistics

Kind: statistic
Spelled: snr, s/n, sbr, cnr

As YAML for a pack file

  - {term: signal_to_noise, theme_kind: statistic, surfaces: [snr, "s/n", sbr, cnr]}

Section page ›

Dictionary word

significance

significance · Core, statistics

Kind: statistic
Spelled: sig, significant, ns, nonsignificant, alpha

As YAML for a pack file

  - {term: significance, theme_kind: statistic, surfaces: [sig, significant, ns, nonsignificant,
     alpha]}

Section page ›

Dictionary word

single

single · Core, process

Kind: quantifier
Spelled: single

As YAML for a pack file

  - {term: single, theme_kind: quantifier, surfaces: [single]}

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Dictionary word

skipped

skipped · Core, process

Kind: status
Spelled: skipped, skip, bypassed, excluded

As YAML for a pack file

  - {term: skipped, theme_kind: status, surfaces: [skipped, skip, bypassed, excluded]}

Section page ›

Dictionary word

slide

slide · Core, process

Kind: vessel
Spelled: slide, slides, coverslip, chamber, dish, flask, tube, vial

As YAML for a pack file

  - {term: slide, theme_kind: vessel, surfaces: [slide, slides, coverslip, chamber, dish, flask,
     tube, vial]}

Section page ›

Dictionary word

slope

slope · Core, statistics

Kind: statistic
Spelled: slope, gradient, m_coef

As YAML for a pack file

  - {term: slope, theme_kind: statistic, surfaces: [slope, gradient, m_coef]}

Section page ›

Dictionary word

smoothed

smoothed · Core, process

Kind: stage
Spelled: smooth, smoothed, smoothing

As YAML for a pack file

  - {term: smoothed, theme_kind: stage, surfaces: [smooth, smoothed, smoothing]}

Section page ›

Dictionary word

specificity

specificity · Core, statistics

Kind: statistic
Spelled: specificity, tnr

As YAML for a pack file

  - {term: specificity, theme_kind: statistic, surfaces: [specificity, tnr]}

Section page ›

Dictionary word

SQL

sql_source · Core, formats

Kind: format
Spelled: sql

As YAML for a pack file

  - {term: sql_source, canonical: SQL, theme_kind: format, surfaces: [sql], program: true}

Section page ›

Dictionary word

stage

stage · Core, instruments

Kind: instrument
Spelled: stage, xystage, zstage, piezo, motorised, motorized

As YAML for a pack file

  - {term: stage, theme_kind: instrument, surfaces: [stage, xystage, zstage, piezo, motorised,
     motorized]}

Section page ›

Dictionary word

standard deviation

standard_deviation · Core, statistics

Kind: statistic
Spelled: sd, std, stdev, stddev, sigma

As YAML for a pack file

  - {term: standard_deviation, theme_kind: statistic, surfaces: [sd, std, stdev, stddev, sigma]}

Section page ›

Dictionary word

standard error

standard_error · Core, statistics

Kind: statistic
Spelled: se, sem, stderr

As YAML for a pack file

  - {term: standard_error, theme_kind: statistic, surfaces: [se, sem, stderr]}

Section page ›

Dictionary word

stated replicate count

stated_replicate_count · Core, time and versions

Kind: count
Spelled: n
Ambiguous: Yes. Also read as count

As YAML for a pack file

  - {term: stated_replicate_count, theme_kind: count, surfaces: ["n"], ambiguous_with: [count]}

Section page ›

Dictionary word

step size

step_size · Core, statistics

Kind: statistic
Spelled: step_size, step_sizes, step-size, step-sizes

As YAML for a pack file

  - {term: step_size, theme_kind: statistic, surfaces: [step_size, step_sizes, "step-size",
     "step-sizes"]}

Section page ›

Dictionary word

stitched

stitched · Core, process

Kind: stage
Spelled: stitch, stitched, stitching, mosaic

As YAML for a pack file

  - {term: stitched, theme_kind: stage, surfaces: [stitch, stitched, stitching, mosaic]}

Section page ›

Dictionary word

structured format

structured_format · Core, formats

Kind: format
Spelled: json, yaml_format, toml_format, xml_format, ini_format, protobuf

As YAML for a pack file

  - {term: structured_format, theme_kind: format, surfaces: [json, yaml_format, toml_format,
     xml_format, ini_format, protobuf]}

Section page ›

Dictionary word

study

study · Core, process

Kind: experiment
Spelled: study, studies, investigation

As YAML for a pack file

  - {term: study, theme_kind: experiment, surfaces: [study, studies, investigation]}

Section page ›

Dictionary word

subject

subject · Core, process

Kind: subject
Spelled: subject, subjects, animal, animals, donor, donors

As YAML for a pack file

  - {term: subject, theme_kind: subject, surfaces: [subject, subjects, animal, animals, donor,
     donors]}

Section page ›

Dictionary word

subset

subset · Core, process

Kind: stage
Spelled: subset, selection, selected, filtered_subset

As YAML for a pack file

  - {term: subset, theme_kind: stage, surfaces: [subset, selection, selected, filtered_subset]}

Section page ›

Dictionary word

sum

sum · Core, statistics

Kind: statistic
Spelled: sum, total, integral, integrated, auc_area

As YAML for a pack file

  - {term: sum, theme_kind: statistic, surfaces: [sum, total, integral, integrated, auc_area]}

Section page ›

Dictionary word

summary

summary · Core, process

Kind: stage
Spelled: summary, summaries, summarised, summarized, aggregate, aggregated, rollup

As YAML for a pack file

  - {term: summary, theme_kind: stage, surfaces: [summary, summaries, summarised, summarized,
     aggregate, aggregated, rollup]}

Section page ›

Dictionary word

sunday

sunday · Core, time and versions

Kind: date
Spelled: sunday

As YAML for a pack file

  - {term: sunday, theme_kind: date, surfaces: [sunday], weekday: 7, stamp_abbreviation: sun}

Section page ›

Dictionary word

superseded by

superseded_by · Core, negative lexicon

Kind: quality
Spelled: replacedby, replaced-by, supersededby, seeinstead

As YAML for a pack file

  - {term: superseded_by, theme_kind: quality, surfaces: [replacedby, "replaced-by",
     supersededby, seeinstead], strength: strong}

Section page ›

Dictionary word

supplementary

supplementary · Core, file roles

Kind: file role
Spelled: supp, suppl, supplementary, supplement, si, appendix, extended

As YAML for a pack file

  - {term: supplementary, theme_kind: file_role, surfaces: [supp, suppl, supplementary,
     supplement, si, appendix, extended]}

Section page ›

Dictionary word

sync artifact

sync_artifact · Core, filesystem noise

Kind: quality
Spelled: .dropbox, .dropbox.cache, .onedrive, Icon?, conflicted copy, .nfs

As YAML for a pack file

  - {term: sync_artifact, theme_kind: quality, surfaces: [".dropbox", ".dropbox.cache",
     ".onedrive", "Icon?", "conflicted copy", ".nfs"], strength: strong}

Section page ›

Dictionary word

t test

t_test · Core, statistics

Kind: statistic
Spelled: ttest, t-test, students, welch, paired_t

As YAML for a pack file

  - {term: t_test, theme_kind: statistic, surfaces: [ttest, "t-test", students, welch,
     paired_t]}

Section page ›

Dictionary word

table

table · Core, file roles

Kind: file role
Spelled: table, tables, tab, sheet, worksheet, spreadsheet

As YAML for a pack file

  - {term: table, theme_kind: file_role, surfaces: [table, tables, tab, sheet, worksheet,
     spreadsheet]}

Section page ›

Dictionary word

tabular format

tabular_format · Core, formats

Kind: format
Spelled: csv, tsv, parquet, feather, arrow, xlsx, xls, ods

As YAML for a pack file

  - {term: tabular_format, theme_kind: format, surfaces: [csv, tsv, parquet, feather, arrow,
     xlsx, xls, ods], extension_only: [arrow, feather]}

Section page ›

Dictionary word

tebibyte

tebibyte · Core, units

Kind: unit
Spelled: TiB, tebibyte

As YAML for a pack file

  - {term: tebibyte, theme_kind: unit, surfaces: [TiB, tebibyte], dimension: digital_size,
     base: byte, factor: 1099511627776.0, ucum: TiBy}

Section page ›

Dictionary word

technical replicate

technical_replicate · Core, time and versions

Kind: replicate
Spelled: tech, technical, techrep, tr

As YAML for a pack file

  - {term: technical_replicate, theme_kind: replicate, surfaces: [tech, technical, techrep, tr]}

Section page ›

Dictionary word

template

template · Core, file roles

Kind: file role
Spelled: template, templates, boilerplate, blank_form

As YAML for a pack file

  - {term: template, theme_kind: file_role, surfaces: [template, templates, boilerplate,
     blank_form]}

Section page ›

Dictionary word

temporary

temporary · Core, negative lexicon

Kind: quality
Spelled: tmp, temp, temporary, transient, ephemeral

As YAML for a pack file

  - {term: temporary, theme_kind: quality, surfaces: [tmp, temp, temporary, transient,
     ephemeral], strength: strong}

Section page ›

Dictionary word

temporary file

temporary_file · Core, formats

Kind: format
Spelled: tmp

As YAML for a pack file

  - {term: temporary_file, canonical: "temporary file", theme_kind: format, surfaces: [tmp],
     extension_only: [tmp]}

Section page ›

Dictionary word

terabyte

terabyte · Core, units

Kind: unit
Spelled: TB, terabyte

As YAML for a pack file

  - {term: terabyte, theme_kind: unit, surfaces: [TB, terabyte], dimension: digital_size,
     base: byte, factor: "1.0e12", ucum: TBy}

Section page ›

Dictionary word

test artifact

test_artifact · Core, negative lexicon

Kind: quality
Spelled: testfile, test-file, trialrun, dryrun, dry-run, smoketest

As YAML for a pack file

  - {term: test_artifact, theme_kind: quality, surfaces: [testfile, "test-file", trialrun,
     dryrun, "dry-run", smoketest], strength: moderate, ambiguous: true}

Section page ›

Dictionary word

text clipping

text_clipping · Core, formats

Kind: format
Spelled: textclipping

As YAML for a pack file

  - {term: text_clipping, canonical: "text clipping", theme_kind: format,
     surfaces: [textclipping]}

Section page ›

Dictionary word

than

than · Core, connecting words

Kind: connective
Spelled: than

As YAML for a pack file

  - {term: than, theme_kind: connective, surfaces: [than]}

Section page ›

Dictionary word

the

the · Core, connecting words

Kind: connective
Spelled: the

As YAML for a pack file

  - {term: the, theme_kind: connective, surfaces: [the]}

Section page ›

Dictionary word

thermocycler

thermocycler · Core, instruments

Kind: instrument
Spelled: thermocycler, pcrmachine, pcr-machine, cycler, lightcycler, qpcr_machine

As YAML for a pack file

  - {term: thermocycler, theme_kind: instrument, surfaces: [thermocycler, pcrmachine,
     "pcr-machine", cycler, lightcycler, qpcr_machine]}

Section page ›

Dictionary word

threshold

threshold · Core, statistics

Kind: statistic
Spelled: threshold, cutoff, cut-off, gate, gating, limit

As YAML for a pack file

  - {term: threshold, theme_kind: statistic, surfaces: [threshold, cutoff, "cut-off", gate,
     gating, limit]}

Section page ›

Dictionary word

thresholded

thresholded · Core, process

Kind: stage
Spelled: thresh, threshold, thresholded, binarised, binarized

As YAML for a pack file

  - {term: thresholded, theme_kind: stage, surfaces: [thresh, threshold, thresholded, binarised,
     binarized]}

Section page ›

Dictionary word

thumbnail

thumbnail · Core, file roles

Kind: file role
Spelled: thumb, thumbnail, thumbnails, preview, icon, contactsheet

As YAML for a pack file

  - {term: thumbnail, theme_kind: file_role, surfaces: [thumb, thumbnail, thumbnails, preview,
     icon, contactsheet]}

Section page ›

Dictionary word

thursday

thursday · Core, time and versions

Kind: date
Spelled: thursday

As YAML for a pack file

  - {term: thursday, theme_kind: date, surfaces: [thursday], weekday: 4,
     stamp_abbreviation: thu}

Section page ›

Dictionary word

time lag

time_lag · Core, statistics

Kind: statistic
Spelled: tlag, t_lag, time_lag, lag_time, timelag

As YAML for a pack file

  - {term: time_lag, theme_kind: statistic, surfaces: [tlag, t_lag, time_lag, lag_time,
     timelag]}

Section page ›

Dictionary word

timepoint

timepoint · Core, process

Kind: timepoint
Spelled: tp, timepoint, timepoints, time-point, timecourse, timeseries

As YAML for a pack file

  - {term: timepoint, theme_kind: timepoint, surfaces: [tp, timepoint, timepoints, "time-point",
     timecourse, timeseries]}

Section page ›

Dictionary word

to

to · Core, connecting words

Kind: connective
Spelled: to

As YAML for a pack file

  - {term: to, theme_kind: connective, surfaces: [to]}

Section page ›

Dictionary word

today

today · Core, time and versions

Kind: date
Spelled: today

As YAML for a pack file

  - {term: today, theme_kind: date, surfaces: [today]}

Section page ›

Dictionary word

todo

todo · Core, negative lexicon

Kind: quality
Spelled: todo, to-do, pending_work, unfinished, incomplete, halfdone, half-done

As YAML for a pack file

  - {term: todo, theme_kind: quality, surfaces: [todo, "to-do", pending_work, unfinished,
     incomplete, halfdone, "half-done"], strength: moderate}

Section page ›

Dictionary word

TOML

toml_document · Core, formats

Kind: format
Spelled: toml

As YAML for a pack file

  - {term: toml_document, canonical: TOML, theme_kind: format, surfaces: [toml]}

Section page ›

Dictionary word

torr

torr · Core, units

Kind: unit
Spelled: Torr, torr, mmHg

As YAML for a pack file

  - {term: torr, theme_kind: unit, surfaces: [Torr, torr, mmHg], dimension: pressure,
     base: pascal, factor: 133.322, ucum: "mm[Hg]"}

Section page ›

Dictionary word

treatment

treatment · Core, process

Kind: condition
Spelled: treat, treated, treatment, treatments, dosed

As YAML for a pack file

  - {term: treatment, theme_kind: condition, surfaces: [treat, treated, treatment, treatments,
     dosed]}

Section page ›

Dictionary word

trial

trial · Core, time and versions

Kind: replicate
Spelled: trial, trials, attempt, attempts, take, takes

As YAML for a pack file

  - {term: trial, theme_kind: replicate, surfaces: [trial, trials, attempt, attempts, take,
     takes]}

Section page ›

Dictionary word

tris carboxyethyl phosphine

tris_carboxyethyl_phosphine · Core, reagents

Kind: reagent
Spelled: tcep

As YAML for a pack file

  - {term: tris_carboxyethyl_phosphine, theme_kind: reagent, surfaces: [tcep]}

Section page ›

Dictionary word

tuesday

tuesday · Core, time and versions

Kind: date
Spelled: tuesday

As YAML for a pack file

  - {term: tuesday, theme_kind: date, surfaces: [tuesday], weekday: 2, stamp_abbreviation: tue}

Section page ›

Dictionary word

tukey

tukey · Core, statistics

Kind: statistic
Spelled: tukey, hsd, dunnett, scheffe

As YAML for a pack file

  - {term: tukey, theme_kind: statistic, surfaces: [tukey, hsd, dunnett, scheffe]}

Section page ›

Dictionary word

turning angle

turning_angle · Core, statistics

Kind: statistic
Spelled: cos_theta, costheta, turning_angle, turning-angle

As YAML for a pack file

  - {term: turning_angle, theme_kind: statistic, surfaces: [cos_theta, costheta, turning_angle,
     "turning-angle"]}

Section page ›

Dictionary word

unaffiliated

unaffiliated · Core, process

Kind: stage
Spelled: misc, miscellaneous, other, unsorted, unfiled, inbox, dump

As YAML for a pack file

  - {term: unaffiliated, theme_kind: stage, surfaces: [misc, miscellaneous, other, unsorted,
     unfiled, inbox, dump]}

Section page ›

Dictionary word

unsure

unsure · Core, negative lexicon

Kind: quality
Spelled: unsure, uncertain, maybe, perhaps, possibly, probably, might, unclear and 3 more

As YAML for a pack file

  - {term: unsure, theme_kind: quality, surfaces: [unsure, uncertain, maybe, perhaps, possibly,
     probably, might, unclear, ambiguous, tbd, tbc], strength: moderate}

Section page ›

Dictionary word

untitled

untitled · Core, negative lexicon

Kind: quality
Spelled: untitled, unnamed, noname, no-name, nameless

As YAML for a pack file

  - {term: untitled, theme_kind: quality, surfaces: [untitled, unnamed, noname, "no-name",
     nameless], strength: strong}

Section page ›

Dictionary word

upsampled

upsampled · Core, process

Kind: stage
Spelled: upsampled, upsample, interpolated

As YAML for a pack file

  - {term: upsampled, theme_kind: stage, surfaces: [upsampled, upsample, interpolated]}

Section page ›

Dictionary word

use this one

use_this_one · Core, negative lexicon

Kind: quality
Spelled: usethis, use-this, usethisone, thisone, correctone, goodone, latest_good

As YAML for a pack file

  - {term: use_this_one, theme_kind: quality, surfaces: [usethis, "use-this", usethisone,
     thisone, correctone, goodone, latest_good], strength: strong}

Section page ›

Dictionary word

variance

variance · Core, statistics

Kind: statistic
Spelled: var, variance

As YAML for a pack file

  - {term: variance, theme_kind: statistic, surfaces: [var, variance]}

Section page ›

Dictionary word

vehicle

vehicle · Core, process

Kind: condition
Spelled: veh, vehicle, dmso_control, carrier

As YAML for a pack file

  - {term: vehicle, theme_kind: condition, surfaces: [veh, vehicle, dmso_control, carrier]}

Section page ›

Dictionary word

version

version · Core, time and versions

Kind: version
Spelled: v, ver, vers, version

As YAML for a pack file

  - {term: version, theme_kind: version, surfaces: [v, ver, vers, version]}

Section page ›

Dictionary word

version control

version_control · Core, filesystem noise

Kind: quality
Spelled: .git, .svn, .hg, .gitignore, .gitattributes, .gitkeep

As YAML for a pack file

  - {term: version_control, theme_kind: quality, surfaces: [".git", ".svn", ".hg", ".gitignore",
     ".gitattributes", ".gitkeep"], strength: decisive}

Section page ›

Dictionary word

version soup

version_soup · Core, negative lexicon

Kind: quality
Spelled: v2final, v3final, finalv2, final2, final3, newfinal, newnew, newest_new

As YAML for a pack file

  - {term: version_soup, theme_kind: quality, surfaces: [v2final, v3final, finalv2, final2,
     final3, newfinal, newnew, newest_new], strength: strong}

Section page ›

Dictionary word

versus

versus · Core, connecting words

Kind: connective
Spelled: vs, versus

As YAML for a pack file

  - {term: versus, theme_kind: connective, surfaces: [vs, versus]}

Section page ›

Dictionary word

via

via · Core, connecting words

Kind: connective
Spelled: via

As YAML for a pack file

  - {term: via, theme_kind: connective, surfaces: [via]}

Section page ›

Dictionary word

video format

video_format · Core, formats

Kind: format
Spelled: avi, mp4, mov, mkv, webm, wmv

As YAML for a pack file

  - {term: video_format, theme_kind: format, surfaces: [avi, mp4, mov, mkv, webm, wmv]}

Section page ›

Dictionary word

violin plot

violin_plot · Core, file roles

Kind: file role
Spelled: violin, violins, violinplot, violin-plot

As YAML for a pack file

  - {term: violin_plot, theme_kind: file_role, surfaces: [violin, violins, violinplot,
     "violin-plot"], product: true}

Section page ›

Dictionary word

volcano plot

volcano_plot · Core, file roles

Kind: file role
Spelled: volcano, volcanoplot, volcano-plot

As YAML for a pack file

  - {term: volcano_plot, theme_kind: file_role, surfaces: [volcano, volcanoplot, "volcano-plot"],
     product: true}

Section page ›

Dictionary word

volt

volt · Core, units

Kind: unit
Spelled: V, volt, volts

As YAML for a pack file

  - {term: volt, theme_kind: unit, surfaces: [V, volt, volts], dimension: voltage, base: volt,
     factor: 1.0, ucum: V}

Section page ›

Dictionary word

voxel

voxel · Core, units

Kind: unit
Spelled: voxel, voxels

As YAML for a pack file

  - {term: voxel, theme_kind: unit, surfaces: [voxel, voxels], dimension: voxels, base: voxel,
     factor: 1.0}

Section page ›

Dictionary word

VTK data

vtk_data · Core, formats

Kind: format
Spelled: vtk

As YAML for a pack file

  - {term: vtk_data, canonical: "VTK data", theme_kind: format, surfaces: [vtk],
     extension_only: true}

Section page ›

Dictionary word

watt

watt · Core, units

Kind: unit
Spelled: W, watt, watts

As YAML for a pack file

  - {term: watt, theme_kind: unit, surfaces: [W, watt, watts], dimension: power, base: watt,
     factor: 1.0, ucum: W}

Section page ›

Dictionary word

web shortcut

web_shortcut · Core, formats

Kind: format
Spelled: webloc

As YAML for a pack file

  - {term: web_shortcut, canonical: "web shortcut", theme_kind: format, surfaces: [webloc]}

Section page ›

Dictionary word

wednesday

wednesday · Core, time and versions

Kind: date
Spelled: wednesday

As YAML for a pack file

  - {term: wednesday, theme_kind: date, surfaces: [wednesday], weekday: 3,
     stamp_abbreviation: wed}

Section page ›

Dictionary word

week

week · Core, units

Kind: unit
Spelled: wk, week, weeks

As YAML for a pack file

  - {term: week, theme_kind: unit, surfaces: [wk, week, weeks], dimension: time, base: second,
     factor: 604800.0, ucum: wk}

Section page ›

Dictionary word

well

well · Core, process

Kind: vessel
Spelled: well, wells

As YAML for a pack file

  - {term: well, theme_kind: vessel, surfaces: [well, wells]}

Section page ›

Dictionary word

wheel

python_wheel · Core, formats

Kind: format
Spelled: whl

As YAML for a pack file

  - {term: python_wheel, canonical: wheel, theme_kind: format, surfaces: [whl], program: true}

Section page ›

Dictionary word

wild type

wild_type · Core, process

Kind: condition
Spelled: wildtype, wild-type, wt

As YAML for a pack file

  - {term: wild_type, canonical: "wild type", theme_kind: condition, surfaces: [wildtype,
     "wild-type", wt]}

Section page ›

Dictionary word

windows metadata

windows_metadata · Core, filesystem noise

Kind: quality
Spelled: Thumbs.db, desktop.ini, ehthumbs.db, $RECYCLE.BIN, System Volume Information

As YAML for a pack file

  - {term: windows_metadata, theme_kind: quality, surfaces: ["Thumbs.db", "desktop.ini",
     "ehthumbs.db", "$RECYCLE.BIN", "System Volume Information"], strength: decisive}

Section page ›

Dictionary word

with

with · Core, connecting words

Kind: connective
Spelled: with

As YAML for a pack file

  - {term: with, theme_kind: connective, surfaces: [with]}

Section page ›

Dictionary word

without

without · Core, connecting words

Kind: connective
Spelled: without

As YAML for a pack file

  - {term: without, theme_kind: connective, surfaces: [without]}

Section page ›

Dictionary word

word processor document

rich_document · Core, formats

Kind: format
Spelled: docx, doc, odt, rtf

As YAML for a pack file

  - {term: rich_document, canonical: "word processor document", theme_kind: format,
     surfaces: [docx, doc, odt, rtf]}

Section page ›

Dictionary word

workstation

workstation · Core, instruments

Kind: instrument
Spelled: workstation, desktop_machine, laptop, server, node, cluster, hpc, gpu_node

As YAML for a pack file

  - {term: workstation, theme_kind: instrument, surfaces: [workstation, desktop_machine, laptop,
     server, node, cluster, hpc, gpu_node]}

Section page ›

Dictionary word

wrong

wrong · Core, negative lexicon

Kind: quality
Spelled: wrong, incorrect, mistake, mistaken, oops, whoops

As YAML for a pack file

  - {term: wrong, theme_kind: quality, surfaces: [wrong, incorrect, mistake, mistaken, oops,
     whoops], strength: strong}

Section page ›

Dictionary word

XML

xml_document · Core, formats

Kind: format
Spelled: xml, xsd, xsl

As YAML for a pack file

  - {term: xml_document, canonical: XML, theme_kind: format, surfaces: [xml, xsd, xsl]}

Section page ›

Dictionary word

YAML

yaml_document · Core, formats

Kind: format
Spelled: yaml, yml

As YAML for a pack file

  - {term: yaml_document, canonical: YAML, theme_kind: format, surfaces: [yaml, yml]}

Section page ›

Dictionary word

year

year · Core, units

Kind: unit
Spelled: y, yr, year, years

As YAML for a pack file

  - {term: year, theme_kind: unit, surfaces: ["y", yr, year, years], dimension: time,
     base: second, factor: 31557600.0, ucum: a}

Section page ›

Dictionary word

yesterday

yesterday · Core, time and versions

Kind: date
Spelled: yesterday

As YAML for a pack file

  - {term: yesterday, theme_kind: date, surfaces: [yesterday]}

Section page ›

Dictionary word

zscore

zscore · Core, statistics

Kind: statistic
Spelled: z, zscore, z-score, standardised, standardized

As YAML for a pack file

  - {term: zscore, theme_kind: statistic, surfaces: [z, zscore, "z-score", standardised,
     standardized]}

Section page ›

Microscopy pack 80 words

Imaging modalities, optical configuration, labels and image processing. Version 3. A project loads a pack by name. Pack page

Word	Kind	Means	Pack
airyscan	technique	Spelled `airyscan`, `airy-scan`, `isim`, `rescan`	Microscopy pack
atomic force microscopy	technique	Spelled `afm`, `scanningprobe`	Microscopy pack
background subtraction	technique	Spelled `bgsub`, `background-subtracted`, `rollingball`, `rolling-ball`, `tophat`	Microscopy pack
binning	technique	Spelled `bin1`, `bin2`, `bin4`, `binning`	Microscopy pack
bleach correction	technique	Spelled `bleachcorrect`, `bleach-corrected`, `photobleach_correction`	Microscopy pack
brightfield	technique	Spelled `bf`, `brightfield`, `bright-field`, `transmitted`, `trans`	Microscopy pack
calcium imaging	technique	Spelled `calcium imaging`, `ca_imaging`, `gcamp_class`, `gcamp`, `gcamp6` and 9 more	Microscopy pack
channel	channel	Spelled `ch`, `chan`, `channel`, `c0`, `c1` and 6 more	Microscopy pack
colocalisation	technique	Spelled `coloc`, `colocalisation`, `colocalization`, `pearson_coloc`, `manders` and 1 more	Microscopy pack
confocal	technique	Spelled `confocal`, `lsm`, `clsm`, `pointscanning`, `point-scanning`	Microscopy pack
correlation spectroscopy	technique	Spelled `fcs`, `fccs`, `rics`, `n&b`, `numberandbrightness`	Microscopy pack
correlative	technique	Spelled `clem`, `correlative`, `correlative-light-electron`	Microscopy pack
CryoCLEM `cryo_correlative`	technique	Spelled `cryo-clem`, `cryo-correlative`	Microscopy pack
CryoEM `cryo_electron_microscopy`	technique	Spelled `cryoem`, `cryo-em`, `cryo-tem`, `cryo-electron microscopy`, `electron cryo-microscopy` and 7 more	Microscopy pack
CryoET `cryo_electron_tomography`	technique	Spelled `cryo-et`, `cryo-electron tomography`, `electron cryo-tomography`, `cryo-tomography`, `cryo-electron tomogram` and 7 more	Microscopy pack
CryoFIB `cryo_focused_ion_beam`	technique	Spelled `cryo-fib`, `cryo-fib-sem`, `cryo-plasma-fib`, `cryo serial fib`, `cryo-fib-sem serial` and 1 more	Microscopy pack
darkfield	technique	Spelled `df`, `darkfield`, `dark-field`	Microscopy pack
deconvolution method	technique	Spelled `rl_decon`, `richardson`, `lucy`, `huygens_style`, `blinddecon`	Microscopy pack
differential interference contrast	technique	Spelled `dic`, `nomarski`	Microscopy pack
drift correction	technique	Spelled `driftcorrect`, `drift-corrected`, `stabilised`, `stabilized`, `registration_drift`	Microscopy pack
electron density map `em_density_format`	format	Spelled `mrc`, `ccp4`	Microscopy pack
electron microscopy	technique	Spelled `em`, `sem`, `electron microscopy`, `electron microscope`, `scanning electron microscopy` and 5 more	Microscopy pack
energy transfer	technique	Spelled `fret`, `bret`, `acceptor_photobleach`, `sensitised_emission`	Microscopy pack
epifluorescence	technique	Spelled `epi`, `epifluorescence`, `widefield`, `wide-field`, `wf` and 4 more	Microscopy pack
EVOS acquisition record `evos_acquisition`	format	Spelled `timelapse`, `routine`	Microscopy pack
expansion microscopy	technique	Spelled `exm`, `expansion`, `expansion-microscopy`	Microscopy pack
exposure	technique	Spelled `exp_time`, `exposure`, `integration_time`, `dwell`, `dwelltime`	Microscopy pack
field of view	acquisition	Spelled `fov`, `field`, `frame_area`, `view`	Microscopy pack
Fiji ROI archive `fiji_roi_zip`	format	Spelled `fiji_roi_zip`	Microscopy pack
flat field	technique	Spelled `ffc`, `flatfield`, `flat-field`, `shading`, `shadingcorrection` and 1 more	Microscopy pack
fluorescence lifetime	technique	Spelled `flim`, `tcspc`, `lifetime`	Microscopy pack
fluorescent protein	reagent	Spelled `gfp`, `egfp`, `sfgfp`, `megfp`, `halo tag` and 17 more	Microscopy pack
gain	technique	Spelled `gain`, `emgain`, `em-gain`, `offset_gain`, `iso`	Microscopy pack
HILO `highly_inclined_illumination`	technique	Spelled `hilo`, `highly inclined and laminated optical sheet`, `highly inclined thin illumination`	Microscopy pack
image stack	acquisition	Spelled `timelapse`, `time-lapse`, `time_lapse`, `imagestack`, `image-stack` and 2 more	Microscopy pack
ImageJ region of interest `imagej_roi`	format	Spelled `roi`	Microscopy pack
immersion	technique	Spelled `oil`, `water`, `glycerol`, `silicone`, `air` and 3 more	Microscopy pack
immunolabel	reagent	Spelled `immunofluorescence`, `if_stain`, `immunostain`, `immunohistochemistry`, `ihc` and 2 more	Microscopy pack
intensity measure	technique	Spelled `intensity`, `intensities`, `meanintensity`, `integrateddensity`, `intden` and 6 more	Microscopy pack
laser power	technique	Spelled `power`, `laserpower`, `laser-power`, `intensity_setting`, `percent_power`	Microscopy pack
light microscopy	technique	Spelled `light microscopy`	Microscopy pack
light sheet	technique	Spelled `lightsheet`, `light-sheet`, `lsfm`, `spim`, `dslm` and 2 more	Microscopy pack
maximum projection	technique	Spelled `mip`, `maxproj`, `max-projection`, `maximum_intensity`, `sumproj` and 3 more	Microscopy pack
MitoGraph output `mitograph_output`	format	Spelled `coo`, `gnet`, `mitograph`	Microscopy pack
multipoint	acquisition	Spelled `multipoint`, `xy`, `xyz`, `positions`, `stagepositions` and 1 more	Microscopy pack
nuclear stain	reagent	Spelled `dapi`, `hoechst`, `hoechst 33342`, `hoechst 33258`, `bisbenzimide` and 5 more	Microscopy pack
organelle tracker	reagent	Spelled `mitotracker`, `lysotracker`, `ertracker`, `mito tracker`, `lyso tracker` and 6 more	Microscopy pack
orthogonal view	technique	Spelled `ortho`, `orthogonal`, `xz`, `yz`, `resliced` and 1 more	Microscopy pack
phase contrast	technique	Spelled `ph`, `phase`, `phasecontrast`, `phase-contrast`, `ph1` and 2 more	Microscopy pack
phase plate	technique	Spelled `phase plate`	Microscopy pack
photoactivation	technique	Spelled `photoactivation`, `photoconversion`, `paGFP_class`, `optogenetic_stim`	Microscopy pack
photobleaching recovery	technique	Spelled `frap`, `flip`, `fluorescence_recovery`, `fluorescence recovery after photobleaching`	Microscopy pack
pinhole	technique	Spelled `pinhole`, `airy_units`, `au_pinhole`	Microscopy pack
pixel size	technique	Spelled `pixelsize`, `pixel-size`, `xyres`, `zstep`, `z-step` and 2 more	Microscopy pack
quantum dot	reagent	Spelled `quantum dot`, `qdot`	Microscopy pack
ratiometric	technique	Spelled `ratiometric`, `ratio_imaging`, `fura_style`, `pericam_style`	Microscopy pack
region of interest	acquisition	Spelled `roi`, `rois`, `region`, `regions`, `bounding_box` and 1 more	Microscopy pack
segmentation method	technique	Spelled `otsu`, `watershed`, `cellpose`, `stardist`, `ilastik` and 3 more	Microscopy pack
single molecule localisation	technique	Spelled `palm`, `storm`, `dstorm`, `smlm`, `paint` and 5 more	Microscopy pack
single particle	technique	Spelled `single particle`	Microscopy pack
single particle tracking	technique	Spelled `spt`, `smt`, `single particle tracking`, `single molecule tracking`, `tracking` and 4 more	Microscopy pack
skeletonised shape `skeleton`	technique	Spelled `skeleton`, `skeletons`, `skeletonised`, `skeletonized`	Microscopy pack
spinning disk	technique	Spelled `sd`, `spinningdisk`, `spinning-disk`, `csu`, `yokogawa_style`	Microscopy pack
stimulated emission depletion	technique	Spelled `sted`, `resolft`	Microscopy pack
structured illumination	technique	Spelled `sim`, `structured-illumination`, `apotome`	Microscopy pack
synthetic dye	reagent	Spelled `tmr`, `tetramethylrhodamine`, `alexa`, `atto`, `cf_dye` and 14 more	Microscopy pack
tile	acquisition	Spelled `tile`, `tiles`, `tiled`, `mosaic`, `montage` and 2 more	Microscopy pack
time series	acquisition	Spelled `t`, `tp`, `timeseries`, `movie_series`	Microscopy pack
total internal reflection	technique	Spelled `tirf`, `tirfm`	Microscopy pack
tracking method	technique	Spelled `trackpy`, `btrack`, `lap_tracker`, `kalman`, `linking`	Microscopy pack
transmission electron microscopy	technique	Spelled `tem`, `transmission electron microscopy`, `transmission electron microscope`, `transmission-em`	Microscopy pack
trial acquisition	acquisition	Spelled `test`	Microscopy pack
two photon	technique	Spelled `2p`, `twophoton`, `two-photon`, `multiphoton`, `mp` and 1 more	Microscopy pack
viability stain	reagent	Spelled `calcein`, `annexin`, `live_dead`, `live-dead`, `trypanblue` and 3 more	Microscopy pack
wavelength	channel	Spelled `ex`, `em`, `excitation`, `emission`, `nm_line` and 6 more	Microscopy pack
working distance	technique	Spelled `wd`, `working-distance`	Microscopy pack
X-ray tomography `x_ray_tomography`	technique	Spelled `x-ray tomography`, `x-ray tomogram`, `x-ray tomo`, `x-ray ct`, `x-ray microtomography` and 6 more	Microscopy pack
z stack	acquisition	Spelled `z`, `zs`, `zstack`, `z-stack`, `zseries` and 6 more	Microscopy pack
Zeiss LSM overlay `zeiss_lsm_overlay`	format	Spelled `ovl`	Microscopy pack
Zeiss ZEN graphics export `zeiss_zen_graphics`	format	Spelled `cz`	Microscopy pack

Dictionary word

airyscan

airyscan · Microscopy pack

Kind: technique
Spelled: airyscan, airy-scan, isim, rescan

As YAML for a pack file

  - {term: airyscan, theme_kind: technique, surfaces: [airyscan, "airy-scan", isim, rescan]}

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Dictionary word

atomic force microscopy

atomic_force_microscopy · Microscopy pack

Kind: technique
Spelled: afm, scanningprobe

As YAML for a pack file

  - {term: atomic_force_microscopy, theme_kind: technique, surfaces: [afm, scanningprobe]}

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Dictionary word

background subtraction

background_subtraction · Microscopy pack

Kind: technique
Spelled: bgsub, background-subtracted, rollingball, rolling-ball, tophat
Ambiguous: Yes. Also read as alignment

As YAML for a pack file

  - {term: background_subtraction, theme_kind: technique, surfaces: [bgsub,
     "background-subtracted", rollingball, "rolling-ball", tophat], ambiguous_with: [alignment]}

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Dictionary word

binning

binning · Microscopy pack

Kind: technique
Spelled: bin1, bin2, bin4, binning

As YAML for a pack file

  - {term: binning, theme_kind: technique, surfaces: [bin1, bin2, bin4, binning]}

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Dictionary word

bleach correction

bleach_correction · Microscopy pack

Kind: technique
Spelled: bleachcorrect, bleach-corrected, photobleach_correction

As YAML for a pack file

  - {term: bleach_correction, theme_kind: technique, surfaces: [bleachcorrect,
     "bleach-corrected", photobleach_correction]}

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Dictionary word

brightfield

brightfield · Microscopy pack

Kind: technique
Spelled: bf, brightfield, bright-field, transmitted, trans

As YAML for a pack file

  - {term: brightfield, theme_kind: technique, surfaces: [bf, brightfield, "bright-field",
     transmitted, trans]}

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Dictionary word

calcium imaging

calcium_imaging · Microscopy pack

Kind: technique
Spelled: calcium imaging, ca_imaging, gcamp_class, gcamp, gcamp6, gcamp6f, gcamp6s, gcamp6m and 6 more

As YAML for a pack file

  - {term: calcium_imaging, theme_kind: technique, surfaces: ["calcium imaging", ca_imaging,
     gcamp_class, gcamp, gcamp6, gcamp6f, gcamp6s, gcamp6m, jgcamp7, jgcamp8, "fluo-4", "fluo-3",
     "cal-520", transients]}

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Dictionary word

channel

channel · Microscopy pack

Kind: channel
Spelled: ch, chan, channel, c0, c1, c2, c3, c4 and 3 more

As YAML for a pack file

  - {term: channel, theme_kind: channel, surfaces: [ch, chan, channel, c0, c1, c2, c3, c4, w1,
     w2, w3]}

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Dictionary word

colocalisation

colocalisation · Microscopy pack

Kind: technique
Spelled: coloc, colocalisation, colocalization, pearson_coloc, manders, li_ica

As YAML for a pack file

  - {term: colocalisation, theme_kind: technique, surfaces: [coloc, colocalisation,
     colocalization, pearson_coloc, manders, li_ica]}

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Dictionary word

confocal

confocal · Microscopy pack

Kind: technique
Spelled: confocal, lsm, clsm, pointscanning, point-scanning

As YAML for a pack file

  - {term: confocal, theme_kind: technique, surfaces: [confocal, lsm, clsm, pointscanning,
     "point-scanning"]}

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Dictionary word

correlation spectroscopy

correlation_spectroscopy · Microscopy pack

Kind: technique
Spelled: fcs, fccs, rics, n&b, numberandbrightness

As YAML for a pack file

  - {term: correlation_spectroscopy, theme_kind: technique, surfaces: [fcs, fccs, rics, "n&b",
     numberandbrightness]}

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Dictionary word

correlative

correlative · Microscopy pack

Kind: technique
Spelled: clem, correlative, correlative-light-electron

As YAML for a pack file

  - {term: correlative, theme_kind: technique, surfaces: [clem, correlative,
     "correlative-light-electron"]}

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Dictionary word

CryoCLEM

cryo_correlative · Microscopy pack

Kind: technique
Spelled: cryo-clem, cryo-correlative

As YAML for a pack file

  - {term: cryo_correlative, canonical: CryoCLEM, theme_kind: technique, surfaces: ["cryo-clem",
     "cryo-correlative"]}

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Dictionary word

CryoEM

cryo_electron_microscopy · Microscopy pack

Kind: technique
Spelled: cryoem, cryo-em, cryo-tem, cryo-electron microscopy, electron cryo-microscopy, cryo-electron, cryogenic electron microscopy, cryogenic-em and 4 more

As YAML for a pack file

  - {term: cryo_electron_microscopy, canonical: CryoEM, theme_kind: technique, surfaces: [cryoem,
     "cryo-em", "cryo-tem", "cryo-electron microscopy", "electron cryo-microscopy", "cryo-electron",
     "cryogenic electron microscopy", "cryogenic-em", "cryo-electron microscope",
     "cryo-transmission electron microscopy", "cryo-micrograph", "cryo-sem"]}

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Dictionary word

CryoET

cryo_electron_tomography · Microscopy pack

Kind: technique
Spelled: cryo-et, cryo-electron tomography, electron cryo-tomography, cryo-tomography, cryo-electron tomogram, cryo-tomogram, cryo-electron tomographic, cryo-transmission electron tomography and 4 more

As YAML for a pack file

  - {term: cryo_electron_tomography, canonical: CryoET, theme_kind: technique,
     surfaces: ["cryo-et", "cryo-electron tomography", "electron cryo-tomography", "cryo-tomography",
     "cryo-electron tomogram", "cryo-tomogram", "cryo-electron tomographic",
     "cryo-transmission electron tomography", "cryo-transmission electron tomogram",
     "cryogenic electron tomography", "cryogenic electron tomogram", "cryogenic electron tomograph"]}

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Dictionary word

CryoFIB

cryo_focused_ion_beam · Microscopy pack

Kind: technique
Spelled: cryo-fib, cryo-fib-sem, cryo-plasma-fib, cryo serial fib, cryo-fib-sem serial, cryo-pfib

As YAML for a pack file

  - {term: cryo_focused_ion_beam, canonical: CryoFIB, theme_kind: technique,
     surfaces: ["cryo-fib", "cryo-fib-sem", "cryo-plasma-fib", "cryo serial fib",
     "cryo-fib-sem serial", "cryo-pfib"]}

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Dictionary word

darkfield

darkfield · Microscopy pack

Kind: technique
Spelled: df, darkfield, dark-field

As YAML for a pack file

  - {term: darkfield, theme_kind: technique, surfaces: [df, darkfield, "dark-field"]}

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Dictionary word

deconvolution method

deconvolution_method · Microscopy pack

Kind: technique
Spelled: rl_decon, richardson, lucy, huygens_style, blinddecon

As YAML for a pack file

  - {term: deconvolution_method, theme_kind: technique, surfaces: [rl_decon, richardson, lucy,
     huygens_style, blinddecon]}

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Dictionary word

differential interference contrast

differential_interference_contrast · Microscopy pack

Kind: technique
Spelled: dic, nomarski

As YAML for a pack file

  - {term: differential_interference_contrast, theme_kind: technique, surfaces: [dic, nomarski]}

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Dictionary word

drift correction

drift_correction · Microscopy pack

Kind: technique
Spelled: driftcorrect, drift-corrected, stabilised, stabilized, registration_drift

As YAML for a pack file

  - {term: drift_correction, theme_kind: technique, surfaces: [driftcorrect, "drift-corrected",
     stabilised, stabilized, registration_drift]}

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Dictionary word

electron density map

em_density_format · Microscopy pack

Kind: format
Spelled: mrc, ccp4

As YAML for a pack file

  - {term: em_density_format, canonical: "electron density map", theme_kind: format,
     surfaces: [mrc, ccp4]}

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Dictionary word

electron microscopy

electron_microscopy · Microscopy pack

Kind: technique
Spelled: em, sem, electron microscopy, electron microscope, scanning electron microscopy, electron tomography, fibsem, fib-sem and 2 more

As YAML for a pack file

  - {term: electron_microscopy, theme_kind: technique, surfaces: [em, sem, "electron microscopy",
     "electron microscope", "scanning electron microscopy", "electron tomography", fibsem, "fib-sem",
     sbfsem, tomography]}

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Dictionary word

energy transfer

energy_transfer · Microscopy pack

Kind: technique
Spelled: fret, bret, acceptor_photobleach, sensitised_emission

As YAML for a pack file

  - {term: energy_transfer, theme_kind: technique, surfaces: [fret, bret, acceptor_photobleach,
     sensitised_emission]}

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Dictionary word

epifluorescence

epifluorescence · Microscopy pack

Kind: technique
Spelled: epi, epifluorescence, widefield, wide-field, wf, fluo, fluorescence, fluorescence microscopy and 1 more

As YAML for a pack file

  - {term: epifluorescence, theme_kind: technique, surfaces: [epi, epifluorescence, widefield,
     "wide-field", wf, fluo, fluorescence, "fluorescence microscopy", "widefield microscopy"]}

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Dictionary word

EVOS acquisition record

evos_acquisition · Microscopy pack

Kind: format
Spelled: timelapse, routine

As YAML for a pack file

  - {term: evos_acquisition, canonical: "EVOS acquisition record", theme_kind: format,
     surfaces: [timelapse, routine], extension_only: [timelapse, routine]}

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Dictionary word

expansion microscopy

expansion_microscopy · Microscopy pack

Kind: technique
Spelled: exm, expansion, expansion-microscopy

As YAML for a pack file

  - {term: expansion_microscopy, theme_kind: technique, surfaces: [exm, expansion,
     "expansion-microscopy"]}

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Dictionary word

exposure

exposure · Microscopy pack

Kind: technique
Spelled: exp_time, exposure, integration_time, dwell, dwelltime

As YAML for a pack file

  - {term: exposure, theme_kind: technique, surfaces: [exp_time, exposure, integration_time,
     dwell, dwelltime]}

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Dictionary word

field of view

field_of_view · Microscopy pack

Kind: acquisition
Spelled: fov, field, frame_area, view

As YAML for a pack file

  - {term: field_of_view, theme_kind: acquisition, surfaces: [fov, field, frame_area, view]}

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Dictionary word

Fiji ROI archive

fiji_roi_zip · Microscopy pack

Kind: format
Spelled: fiji_roi_zip

As YAML for a pack file

  - {term: fiji_roi_zip, canonical: "Fiji ROI archive", theme_kind: format,
     surfaces: [fiji_roi_zip], extension_only: true}

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Dictionary word

flat field

flat_field · Microscopy pack

Kind: technique
Spelled: ffc, flatfield, flat-field, shading, shadingcorrection, illumination_correction

As YAML for a pack file

  - {term: flat_field, theme_kind: technique, surfaces: [ffc, flatfield, "flat-field", shading,
     shadingcorrection, illumination_correction]}

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Dictionary word

fluorescence lifetime

fluorescence_lifetime · Microscopy pack

Kind: technique
Spelled: flim, tcspc, lifetime

As YAML for a pack file

  - {term: fluorescence_lifetime, theme_kind: technique, surfaces: [flim, tcspc, lifetime]}

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Dictionary word

fluorescent protein

fluorescent_protein · Microscopy pack

Kind: reagent
Spelled: gfp, egfp, sfgfp, megfp, halo tag, yfp, cfp, bfp and 14 more

As YAML for a pack file

  - {term: fluorescent_protein, theme_kind: reagent, surfaces: [gfp, egfp, sfgfp, megfp,
     "halo tag", yfp, cfp, bfp, rfp, mcherry, mscarlet, mneongreen, tdtomato, dsred, mkate,
     mturquoise, venus, citrine, cerulean, halo, snap, clip], signed: true}

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Dictionary word

gain

gain · Microscopy pack

Kind: technique
Spelled: gain, emgain, em-gain, offset_gain, iso

As YAML for a pack file

  - {term: gain, theme_kind: technique, surfaces: [gain, emgain, "em-gain", offset_gain, iso]}

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Dictionary word

HILO

highly_inclined_illumination · Microscopy pack

Kind: technique
Spelled: hilo, highly inclined and laminated optical sheet, highly inclined thin illumination

As YAML for a pack file

  - {term: highly_inclined_illumination, canonical: HILO, theme_kind: technique, surfaces: [hilo,
     "highly inclined and laminated optical sheet", "highly inclined thin illumination"]}

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Dictionary word

image stack

image_stack · Microscopy pack

Kind: acquisition
Spelled: timelapse, time-lapse, time_lapse, imagestack, image-stack, stack, stacks

As YAML for a pack file

  - {term: image_stack, canonical: "image stack", theme_kind: acquisition, surfaces: [timelapse,
     "time-lapse", time_lapse, imagestack, "image-stack", stack, stacks]}

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Dictionary word

ImageJ region of interest

imagej_roi · Microscopy pack

Kind: format
Spelled: roi

As YAML for a pack file

  - {term: imagej_roi, canonical: "ImageJ region of interest", theme_kind: format,
     surfaces: [roi], extension_only: [roi]}

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Dictionary word

immersion

immersion · Microscopy pack

Kind: technique
Spelled: oil, water, glycerol, silicone, air, dry, immersion, multi-immersion

As YAML for a pack file

  - {term: immersion, theme_kind: technique, surfaces: [oil, water, glycerol, silicone, air, dry,
     immersion, "multi-immersion"]}

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Dictionary word

immunolabel

immunolabel · Microscopy pack

Kind: reagent
Spelled: immunofluorescence, if_stain, immunostain, immunohistochemistry, ihc, primary_ab, secondary_ab

As YAML for a pack file

  - {term: immunolabel, theme_kind: reagent, surfaces: [immunofluorescence, if_stain,
     immunostain, immunohistochemistry, ihc, primary_ab, secondary_ab]}

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Dictionary word

intensity measure

intensity_measure · Microscopy pack

Kind: technique
Spelled: intensity, intensities, meanintensity, integrateddensity, intden, rawintden, area_measure, perimeter and 3 more

As YAML for a pack file

  - {term: intensity_measure, theme_kind: technique, surfaces: [intensity, intensities,
     meanintensity, integrateddensity, intden, rawintden, area_measure, perimeter, circularity,
     aspectratio, feret]}

Section page ›

Dictionary word

laser power

laser_power · Microscopy pack

Kind: technique
Spelled: power, laserpower, laser-power, intensity_setting, percent_power

As YAML for a pack file

  - {term: laser_power, theme_kind: technique, surfaces: [power, laserpower, "laser-power",
     intensity_setting, percent_power]}

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Dictionary word

light microscopy

light_microscopy · Microscopy pack

Kind: technique
Spelled: light microscopy

As YAML for a pack file

  - {term: light_microscopy, canonical: "light microscopy", theme_kind: technique,
     surfaces: ["light microscopy"]}

Section page ›

Dictionary word

light sheet

light_sheet · Microscopy pack

Kind: technique
Spelled: lightsheet, light-sheet, lsfm, spim, dslm, lls, lattice-light-sheet

As YAML for a pack file

  - {term: light_sheet, theme_kind: technique, surfaces: [lightsheet, "light-sheet", lsfm, spim,
     dslm, lls, "lattice-light-sheet"]}

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Dictionary word

maximum projection

maximum_projection · Microscopy pack

Kind: technique
Spelled: mip, maxproj, max-projection, maximum_intensity, sumproj, avgproj, stdproj, maxz

As YAML for a pack file

  - {term: maximum_projection, theme_kind: technique, surfaces: [mip, maxproj, "max-projection",
     maximum_intensity, sumproj, avgproj, stdproj, maxz]}

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Dictionary word

MitoGraph output

mitograph_output · Microscopy pack

Kind: format
Spelled: coo, gnet, mitograph

As YAML for a pack file

  - {term: mitograph_output, canonical: "MitoGraph output", theme_kind: format, surfaces: [coo,
     gnet, mitograph], extension_only: true}

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Dictionary word

multipoint

multipoint · Microscopy pack

Kind: acquisition
Spelled: multipoint, xy, xyz, positions, stagepositions, sites

As YAML for a pack file

  - {term: multipoint, theme_kind: acquisition, surfaces: [multipoint, xy, xyz, positions,
     stagepositions, sites]}

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Dictionary word

nuclear stain

nuclear_stain · Microscopy pack

Kind: reagent
Spelled: dapi, hoechst, hoechst 33342, hoechst 33258, bisbenzimide, draq5, sytox, propidium and 2 more

As YAML for a pack file

  - {term: nuclear_stain, theme_kind: reagent, surfaces: [dapi, hoechst, "hoechst 33342",
     "hoechst 33258", bisbenzimide, draq5, sytox, propidium, pi_stain, todo3]}

Section page ›

Dictionary word

organelle tracker

organelle_tracker · Microscopy pack

Kind: reagent
Spelled: mitotracker, lysotracker, ertracker, mito tracker, lyso tracker, er tracker, golgi_stain, phalloidin and 3 more

As YAML for a pack file

  - {term: organelle_tracker, theme_kind: reagent, surfaces: [mitotracker, lysotracker,
     ertracker, "mito tracker", "lyso tracker", "er tracker", golgi_stain, phalloidin, wga, cellmask,
     membrane_dye]}

Section page ›

Dictionary word

orthogonal view

orthogonal_view · Microscopy pack

Kind: technique
Spelled: ortho, orthogonal, xz, yz, resliced, reslice

As YAML for a pack file

  - {term: orthogonal_view, theme_kind: technique, surfaces: [ortho, orthogonal, xz, yz,
     resliced, reslice]}

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Dictionary word

phase contrast

phase_contrast · Microscopy pack

Kind: technique
Spelled: ph, phase, phasecontrast, phase-contrast, ph1, ph2, ph3

As YAML for a pack file

  - {term: phase_contrast, theme_kind: technique, surfaces: [ph, phase, phasecontrast,
     "phase-contrast", ph1, ph2, ph3]}

Section page ›

Dictionary word

phase plate

phase_plate · Microscopy pack

Kind: technique
Spelled: phase plate

As YAML for a pack file

  - {term: phase_plate, theme_kind: technique, surfaces: ["phase plate"]}

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Dictionary word

photoactivation

photoactivation · Microscopy pack

Kind: technique
Spelled: photoactivation, photoconversion, paGFP_class, optogenetic_stim

As YAML for a pack file

  - {term: photoactivation, theme_kind: technique, surfaces: [photoactivation, photoconversion,
     paGFP_class, optogenetic_stim]}

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Dictionary word

photobleaching recovery

photobleaching_recovery · Microscopy pack

Kind: technique
Spelled: frap, flip, fluorescence_recovery, fluorescence recovery after photobleaching

As YAML for a pack file

  - {term: photobleaching_recovery, theme_kind: technique, surfaces: [frap, flip,
     fluorescence_recovery, "fluorescence recovery after photobleaching"]}

Section page ›

Dictionary word

pinhole

pinhole · Microscopy pack

Kind: technique
Spelled: pinhole, airy_units, au_pinhole

As YAML for a pack file

  - {term: pinhole, theme_kind: technique, surfaces: [pinhole, airy_units, au_pinhole]}

Section page ›

Dictionary word

pixel size

pixel_size · Microscopy pack

Kind: technique
Spelled: pixelsize, pixel-size, xyres, zstep, z-step, stepsize, voxelsize

As YAML for a pack file

  - {term: pixel_size, theme_kind: technique, surfaces: [pixelsize, "pixel-size", xyres, zstep,
     "z-step", stepsize, voxelsize]}

Section page ›

Dictionary word

quantum dot

quantum_dot · Microscopy pack

Kind: reagent
Spelled: quantum dot, qdot

As YAML for a pack file

  - {term: quantum_dot, canonical: "quantum dot", theme_kind: reagent, surfaces: ["quantum dot",
     qdot]}

Section page ›

Dictionary word

ratiometric

ratiometric · Microscopy pack

Kind: technique
Spelled: ratiometric, ratio_imaging, fura_style, pericam_style

As YAML for a pack file

  - {term: ratiometric, theme_kind: technique, surfaces: [ratiometric, ratio_imaging, fura_style,
     pericam_style]}

Section page ›

Dictionary word

region of interest

region_of_interest · Microscopy pack

Kind: acquisition
Spelled: roi, rois, region, regions, bounding_box, bbox

As YAML for a pack file

  - {term: region_of_interest, theme_kind: acquisition, surfaces: [roi, rois, region, regions,
     bounding_box, bbox]}

Section page ›

Dictionary word

segmentation method

segmentation_method · Microscopy pack

Kind: technique
Spelled: otsu, watershed, cellpose, stardist, ilastik, unet, threshold_seg, activecontour

As YAML for a pack file

  - {term: segmentation_method, theme_kind: technique, surfaces: [otsu, watershed, cellpose,
     stardist, ilastik, unet, threshold_seg, activecontour]}

Section page ›

Dictionary word

single molecule localisation

single_molecule_localisation · Microscopy pack

Kind: technique
Spelled: palm, storm, dstorm, smlm, paint, dnapaint, single-molecule localisation, single-molecule localization and 2 more

As YAML for a pack file

  - {term: single_molecule_localisation, theme_kind: technique, surfaces: [palm, storm, dstorm,
     smlm, paint, dnapaint, "single-molecule localisation", "single-molecule localization",
     "single-molecule localisation microscopy", "single-molecule localization microscopy"]}

Section page ›

Dictionary word

single particle

single_particle · Microscopy pack

Kind: technique
Spelled: single particle

As YAML for a pack file

  - {term: single_particle, theme_kind: technique, surfaces: ["single particle"]}

Section page ›

Dictionary word

single particle tracking

single_particle_tracking · Microscopy pack

Kind: technique
Spelled: spt, smt, single particle tracking, single molecule tracking, tracking, trajectories, msd, mean-squared-displacement and 1 more

As YAML for a pack file

  - {term: single_particle_tracking, theme_kind: technique, surfaces: [spt, smt,
     "single particle tracking", "single molecule tracking", tracking, trajectories, msd,
     "mean-squared-displacement", diffusion]}

Section page ›

Dictionary word

skeletonised shape

skeleton · Microscopy pack

Kind: technique
Spelled: skeleton, skeletons, skeletonised, skeletonized

As YAML for a pack file

  - {term: skeleton, canonical: "skeletonised shape", theme_kind: technique, surfaces: [skeleton,
     skeletons, skeletonised, skeletonized]}

Section page ›

Dictionary word

spinning disk

spinning_disk · Microscopy pack

Kind: technique
Spelled: sd, spinningdisk, spinning-disk, csu, yokogawa_style

As YAML for a pack file

  - {term: spinning_disk, theme_kind: technique, surfaces: [sd, spinningdisk, "spinning-disk",
     csu, yokogawa_style]}

Section page ›

Dictionary word

stimulated emission depletion

stimulated_emission_depletion · Microscopy pack

Kind: technique
Spelled: sted, resolft

As YAML for a pack file

  - {term: stimulated_emission_depletion, theme_kind: technique, surfaces: [sted, resolft]}

Section page ›

Dictionary word

structured illumination

structured_illumination · Microscopy pack

Kind: technique
Spelled: sim, structured-illumination, apotome
Ambiguous: Yes. Also read as simulation

As YAML for a pack file

  - {term: structured_illumination, theme_kind: technique, surfaces: [sim,
     "structured-illumination", apotome], ambiguous_with: [simulation]}

Section page ›

Dictionary word

synthetic dye

synthetic_dye · Microscopy pack

Kind: reagent
Spelled: tmr, tetramethylrhodamine, alexa, atto, cf_dye, dylight, janelia_fluor, jf and 11 more

As YAML for a pack file

  - {term: synthetic_dye, theme_kind: reagent, surfaces: [tmr, tetramethylrhodamine, alexa, atto,
     cf_dye, dylight, janelia_fluor, jf, cy2, cy3, cy5, cy7, fitc, tritc, texasred, "texas-red",
     rhodamine, bodipy, coumarin]}

Section page ›

Dictionary word

tile

tile · Microscopy pack

Kind: acquisition
Spelled: tile, tiles, tiled, mosaic, montage, stitchset, grid_scan

As YAML for a pack file

  - {term: tile, theme_kind: acquisition, surfaces: [tile, tiles, tiled, mosaic, montage,
     stitchset, grid_scan]}

Section page ›

Dictionary word

time series

time_series · Microscopy pack

Kind: acquisition
Spelled: t, tp, timeseries, movie_series

As YAML for a pack file

  - {term: time_series, theme_kind: acquisition, surfaces: [t, tp, timeseries, movie_series]}

Section page ›

Dictionary word

total internal reflection

total_internal_reflection · Microscopy pack

Kind: technique
Spelled: tirf, tirfm

As YAML for a pack file

  - {term: total_internal_reflection, theme_kind: technique, surfaces: [tirf, tirfm]}

Section page ›

Dictionary word

tracking method

tracking_method · Microscopy pack

Kind: technique
Spelled: trackpy, btrack, lap_tracker, kalman, linking

As YAML for a pack file

  - {term: tracking_method, theme_kind: technique, surfaces: [trackpy, btrack, lap_tracker,
     kalman, linking]}

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Dictionary word

transmission electron microscopy

transmission_electron_microscopy · Microscopy pack

Kind: technique
Spelled: tem, transmission electron microscopy, transmission electron microscope, transmission-em

As YAML for a pack file

  - {term: transmission_electron_microscopy, canonical: "transmission electron microscopy",
     theme_kind: technique, surfaces: [tem, "transmission electron microscopy",
     "transmission electron microscope", "transmission-em"]}

Section page ›

Dictionary word

trial acquisition

trial_acquisition · Microscopy pack

Kind: acquisition
Spelled: test

As YAML for a pack file

  - {term: trial_acquisition, canonical: "trial acquisition", theme_kind: acquisition,
     surfaces: [test]}

Section page ›

Dictionary word

two photon

two_photon · Microscopy pack

Kind: technique
Spelled: 2p, twophoton, two-photon, multiphoton, mp, 3p

As YAML for a pack file

  - {term: two_photon, theme_kind: technique, surfaces: ["2p", twophoton, "two-photon",
     multiphoton, mp, "3p"]}

Section page ›

Dictionary word

viability stain

viability_stain · Microscopy pack

Kind: reagent
Spelled: calcein, annexin, live_dead, live-dead, trypanblue, edu, brdu, tunel

As YAML for a pack file

  - {term: viability_stain, theme_kind: reagent, surfaces: [calcein, annexin, live_dead,
     "live-dead", trypanblue, edu, brdu, tunel]}

Section page ›

Dictionary word

wavelength

wavelength · Microscopy pack

Kind: channel
Spelled: ex, em, excitation, emission, nm_line, 405, 488, 561 and 3 more

As YAML for a pack file

  - {term: wavelength, theme_kind: channel, surfaces: [ex, em, excitation, emission, nm_line,
     "405", "488", "561", "594", "640", "647"]}

Section page ›

Dictionary word

working distance

working_distance · Microscopy pack

Kind: technique
Spelled: wd, working-distance

As YAML for a pack file

  - {term: working_distance, theme_kind: technique, surfaces: [wd, "working-distance"]}

Section page ›

Dictionary word

X-ray tomography

x_ray_tomography · Microscopy pack

Kind: technique
Spelled: x-ray tomography, x-ray tomogram, x-ray tomo, x-ray ct, x-ray microtomography, micro-ct, soft x-ray tomography, cryo-soft x-ray tomography and 3 more
Ambiguous: Yes. Also read as clinical imaging

As YAML for a pack file

  - {term: x_ray_tomography, canonical: "X-ray tomography", theme_kind: technique,
     surfaces: ["x-ray tomography", "x-ray tomogram", "x-ray tomo", "x-ray ct",
     "x-ray microtomography", "micro-ct", "soft x-ray tomography", "cryo-soft x-ray tomography", sxt,
     "cryo-sxt", "cryo-soft x-ray"], ambiguous_with: [clinical_imaging]}

Section page ›

Dictionary word

z stack

z_stack · Microscopy pack

Kind: acquisition
Spelled: z, zs, zstack, z-stack, zseries, slice, slices, plane and 3 more

As YAML for a pack file

  - {term: z_stack, theme_kind: acquisition, surfaces: [z, zs, zstack, "z-stack", zseries, slice,
     slices, plane, planes, section, optical_section]}

Section page ›

Dictionary word

Zeiss LSM overlay

zeiss_lsm_overlay · Microscopy pack

Kind: format
Spelled: ovl

As YAML for a pack file

  - {term: zeiss_lsm_overlay, canonical: "Zeiss LSM overlay", theme_kind: format,
     surfaces: [ovl]}

Section page ›

Dictionary word

Zeiss ZEN graphics export

zeiss_zen_graphics · Microscopy pack

Kind: format
Spelled: cz

As YAML for a pack file

  - {term: zeiss_zen_graphics, canonical: "Zeiss ZEN graphics export", theme_kind: format,
     surfaces: [cz], extension_only: [cz]}

Section page ›

Sequencing pack 48 words

Library types, platforms, read structure, processing steps and measures. Version 2. A project loads a pack by name. Pack page

Word	Kind	Means	Pack
alignment	technique	Spelled `align`, `aligned`, `bwa`, `bowtie`, `bowtie2` and 8 more	Sequencing pack
alignment format	format	Spelled `sam`, `bam`, `cram`, `bai`, `crai`	Sequencing pack
annotation format	format	Spelled `gtf`, `gff`, `gff3`, `genbank`, `gb` and 2 more	Sequencing pack
annotation tool	technique	Spelled `annotate`, `snpeff`, `vep`, `annovar`, `prokka` and 1 more	Sequencing pack
assembly	technique	Spelled `assembly`, `assembled`, `spades`, `megahit`, `flye` and 4 more	Sequencing pack
barcode	read structure	Spelled `barcode`, `index_seq`, `i7`, `i5`, `dualindex` and 2 more	Sequencing pack
capillary sequencing trace `capillary_trace`	format	Spelled `ab1`	Sequencing pack
chromatin	technique	Spelled `chipseq`, `chip-seq`, `cutandrun`, `cut-and-run`, `cutandtag` and 4 more	Sequencing pack
conformation	technique	Spelled `hic`, `hi-c`, `4c`, `5c`, `capturec` and 1 more	Sequencing pack
coverage	statistic	Spelled `coverage`, `depth`, `meandepth`, `breadth`, `x-coverage`	Sequencing pack
crosslinking	technique	Spelled `clipseq`, `clip-seq`, `parclip`, `iclip`, `eclip` and 1 more	Sequencing pack
deduplication	technique	Spelled `dedup`, `deduplicated`, `markdup`, `rmdup`, `umi_dedup`	Sequencing pack
demultiplexed	technique	Spelled `demux`, `demultiplexed`, `split_by_sample`, `bcl2fastq`, `bclconvert`	Sequencing pack
differential expression	technique	Spelled `deseq`, `deseq2`, `edger`, `limma`, `voom` and 4 more	Sequencing pack
dna sequencing	technique	Spelled `dnaseq`, `wgs`, `wes`, `exome`, `targeted` and 2 more	Sequencing pack
flowcell	read structure	Spelled `flowcell`, `fc`, `cell_id`, `runid`, `run_folder`	Sequencing pack
index read	read structure	Spelled `i1`, `i2`, `index_read`, `barcode_read`	Sequencing pack
interval format	format	Spelled `bed`, `bedgraph`, `bigwig`, `bw`, `wig` and 2 more	Sequencing pack
lane	read structure	Spelled `l001`, `l002`, `l003`, `l004`, `lane` and 1 more	Sequencing pack
long read platform	instrument	Spelled `nanopore`, `ont`, `minion`, `promethion`, `gridion` and 3 more	Sequencing pack
mapping rate	statistic	Spelled `mappingrate`, `mapping-rate`, `alignmentrate`, `uniquelymapped`, `multimapped`	Sequencing pack
matrix format	format	Spelled `mtx`, `h5ad`, `loom`, `rds_matrix`, `anndata`	Sequencing pack
metagenomics	technique	Spelled `metagenome`, `metagenomics`, `16s`, `its`, `shotgun_meta` and 1 more	Sequencing pack
methylation	technique	Spelled `methylseq`, `bisulfite`, `wgbs`, `rrbs`, `emseq` and 1 more	Sequencing pack
multiple alignment format	format	Spelled `aln`, `msa`, `sto`, `stockholm`	Sequencing pack
normalised expression	statistic	Spelled `tpm`, `fpkm`, `rpkm`, `cpm`, `vst` and 2 more	Sequencing pack
other platform	instrument	Spelled `iontorrent`, `ion-torrent`, `bgi`, `mgi`, `element_bio` and 1 more	Sequencing pack
paired end	read structure	Spelled `pe`, `paired`, `pairedend`, `paired-end`	Sequencing pack
peak calling	technique	Spelled `peaks`, `macs`, `macs2`, `macs3`, `seacr` and 2 more	Sequencing pack
provider sequence text `sequence_text`	format	Spelled `seq`	Sequencing pack
quality control	technique	Spelled `fastqc`, `multiqc`, `qc_report`, `qualimap`, `picard_metrics`	Sequencing pack
quality score	statistic	Spelled `phred`, `q20`, `q30`, `mapq`, `basequality`	Sequencing pack
quantification tool	technique	Spelled `featurecounts`, `htseq`, `rsem`, `stringtie`, `cufflinks`	Sequencing pack
read count	statistic	Spelled `readcount`, `rawcounts`, `countmatrix`	Sequencing pack
read format	format	Spelled `fastq`, `fq`, `fasta`, `fa`, `fna` and 3 more	Sequencing pack
read one	read structure	Spelled `_1`, `read1`, `forward`, `fwd`	Sequencing pack
read one	read structure	Spelled `r1`	Sequencing pack
read two	read structure	Spelled `_2`, `read2`, `reverse`, `rev_read`	Sequencing pack
read two	read structure	Spelled `r2`	Sequencing pack
ribosome profiling	technique	Spelled `riboseq`, `ribo-seq`, `tracking_ribosome`	Sequencing pack
rna sequencing	technique	Spelled `rnaseq`, `rna-seq`, `mrnaseq`, `totalrna`, `polya_seq`	Sequencing pack
short read platform	instrument	Spelled `illumina`, `miseq`, `nextseq`, `novaseq`, `hiseq` and 2 more	Sequencing pack
single cell rna	technique	Spelled `scrnaseq`, `sc-rna-seq`, `snrnaseq`, `single-cell rna sequencing`, `single-cell rna-seq` and 5 more	Sequencing pack
single end	read structure	Spelled `se`, `singleend`, `single-end`	Sequencing pack
spatial transcriptomics	technique	Spelled `spatial`, `visium`, `merfish`, `seqfish`, `xenium_class` and 1 more	Sequencing pack
trimming	technique	Spelled `trim`, `trimmed`, `trimmomatic`, `cutadapt`, `fastp` and 2 more	Sequencing pack
variant calling	technique	Spelled `variants`, `gatk`, `freebayes`, `bcftools_call`, `mutect` and 3 more	Sequencing pack
variant format	format	Spelled `vcf`, `bcf`, `gvcf`, `maf`	Sequencing pack

Dictionary word

alignment

alignment · Sequencing pack

Kind: technique
Spelled: align, aligned, bwa, bowtie, bowtie2, star_aligner, hisat, hisat2 and 5 more
Ambiguous: Yes. Also read as background subtraction

As YAML for a pack file

  - {term: alignment, theme_kind: technique, surfaces: [align, aligned, bwa, bowtie, bowtie2,
     star_aligner, hisat, hisat2, minimap, minimap2, salmon, kallisto, tophat],
     ambiguous_with: [background_subtraction]}

Section page ›

Dictionary word

alignment format

alignment_format · Sequencing pack

Kind: format
Spelled: sam, bam, cram, bai, crai

As YAML for a pack file

  - {term: alignment_format, theme_kind: format, surfaces: [sam, bam, cram, bai, crai]}

Section page ›

Dictionary word

annotation format

annotation_format · Sequencing pack

Kind: format
Spelled: gtf, gff, gff3, genbank, gb, gbk, embl

As YAML for a pack file

  - {term: annotation_format, theme_kind: format, surfaces: [gtf, gff, gff3, genbank, gb, gbk,
     embl], extension_only: [gb]}

Section page ›

Dictionary word

annotation tool

annotation_tool · Sequencing pack

Kind: technique
Spelled: annotate, snpeff, vep, annovar, prokka, augustus

As YAML for a pack file

  - {term: annotation_tool, theme_kind: technique, surfaces: [annotate, snpeff, vep, annovar,
     prokka, augustus]}

Section page ›

Dictionary word

assembly

assembly · Sequencing pack

Kind: technique
Spelled: assembly, assembled, spades, megahit, flye, canu, contig, contigs and 1 more

As YAML for a pack file

  - {term: assembly, theme_kind: technique, surfaces: [assembly, assembled, spades, megahit,
     flye, canu, contig, contigs, scaffold]}

Section page ›

Dictionary word

barcode

barcode · Sequencing pack

Kind: read structure
Spelled: barcode, index_seq, i7, i5, dualindex, umi, unique-molecular-identifier

As YAML for a pack file

  - {term: barcode, theme_kind: read_structure, surfaces: [barcode, index_seq, i7, i5, dualindex,
     umi, "unique-molecular-identifier"]}

Section page ›

Dictionary word

capillary sequencing trace

capillary_trace · Sequencing pack

Kind: format
Spelled: ab1

As YAML for a pack file

  - {term: capillary_trace, canonical: "capillary sequencing trace", theme_kind: format,
     surfaces: [ab1]}

Section page ›

Dictionary word

chromatin

chromatin · Sequencing pack

Kind: technique
Spelled: chipseq, chip-seq, cutandrun, cut-and-run, cutandtag, atacseq, atac-seq, faireseq and 1 more

As YAML for a pack file

  - {term: chromatin, theme_kind: technique, surfaces: [chipseq, "chip-seq", cutandrun,
     "cut-and-run", cutandtag, atacseq, "atac-seq", faireseq, dnase]}

Section page ›

Dictionary word

conformation

conformation · Sequencing pack

Kind: technique
Spelled: hic, hi-c, 4c, 5c, capturec, micro_c

As YAML for a pack file

  - {term: conformation, theme_kind: technique, surfaces: [hic, "hi-c", "4c", "5c", capturec,
     micro_c]}

Section page ›

Dictionary word

coverage

coverage · Sequencing pack

Kind: statistic
Spelled: coverage, depth, meandepth, breadth, x-coverage

As YAML for a pack file

  - {term: coverage, theme_kind: statistic, surfaces: [coverage, depth, meandepth, breadth,
     "x-coverage"]}

Section page ›

Dictionary word

crosslinking

crosslinking · Sequencing pack

Kind: technique
Spelled: clipseq, clip-seq, parclip, iclip, eclip, ripseq

As YAML for a pack file

  - {term: crosslinking, theme_kind: technique, surfaces: [clipseq, "clip-seq", parclip, iclip,
     eclip, ripseq]}

Section page ›

Dictionary word

deduplication

deduplication · Sequencing pack

Kind: technique
Spelled: dedup, deduplicated, markdup, rmdup, umi_dedup

As YAML for a pack file

  - {term: deduplication, theme_kind: technique, surfaces: [dedup, deduplicated, markdup, rmdup,
     umi_dedup]}

Section page ›

Dictionary word

demultiplexed

demultiplexed · Sequencing pack

Kind: technique
Spelled: demux, demultiplexed, split_by_sample, bcl2fastq, bclconvert

As YAML for a pack file

  - {term: demultiplexed, theme_kind: technique, surfaces: [demux, demultiplexed,
     split_by_sample, bcl2fastq, bclconvert]}

Section page ›

Dictionary word

differential expression

differential_expression · Sequencing pack

Kind: technique
Spelled: deseq, deseq2, edger, limma, voom, sleuth, degs, diffexpr and 1 more

As YAML for a pack file

  - {term: differential_expression, theme_kind: technique, surfaces: [deseq, deseq2, edger,
     limma, voom, sleuth, degs, diffexpr, diffexp]}

Section page ›

Dictionary word

dna sequencing

dna_sequencing · Sequencing pack

Kind: technique
Spelled: dnaseq, wgs, wes, exome, targeted, amplicon, panel_seq

As YAML for a pack file

  - {term: dna_sequencing, theme_kind: technique, surfaces: [dnaseq, wgs, wes, exome, targeted,
     amplicon, panel_seq]}

Section page ›

Dictionary word

flowcell

flowcell · Sequencing pack

Kind: read structure
Spelled: flowcell, fc, cell_id, runid, run_folder

As YAML for a pack file

  - {term: flowcell, theme_kind: read_structure, surfaces: [flowcell, fc, cell_id, runid,
     run_folder]}

Section page ›

Dictionary word

index read

index_read · Sequencing pack

Kind: read structure
Spelled: i1, i2, index_read, barcode_read

As YAML for a pack file

  - {term: index_read, theme_kind: read_structure, surfaces: [i1, i2, index_read, barcode_read]}

Section page ›

Dictionary word

interval format

interval_format · Sequencing pack

Kind: format
Spelled: bed, bedgraph, bigwig, bw, wig, narrowpeak, broadpeak

As YAML for a pack file

  - {term: interval_format, theme_kind: format, surfaces: [bed, bedgraph, bigwig, bw, wig,
     narrowpeak, broadpeak]}

Section page ›

Dictionary word

lane

lane · Sequencing pack

Kind: read structure
Spelled: l001, l002, l003, l004, lane, lanes

As YAML for a pack file

  - {term: lane, theme_kind: read_structure, surfaces: [l001, l002, l003, l004, lane, lanes]}

Section page ›

Dictionary word

long read platform

long_read_platform · Sequencing pack

Kind: instrument
Spelled: nanopore, ont, minion, promethion, gridion, pacbio, hifi, revio

As YAML for a pack file

  - {term: long_read_platform, theme_kind: instrument, surfaces: [nanopore, ont, minion,
     promethion, gridion, pacbio, hifi, revio]}

Section page ›

Dictionary word

mapping rate

mapping_rate · Sequencing pack

Kind: statistic
Spelled: mappingrate, mapping-rate, alignmentrate, uniquelymapped, multimapped

As YAML for a pack file

  - {term: mapping_rate, theme_kind: statistic, surfaces: [mappingrate, "mapping-rate",
     alignmentrate, uniquelymapped, multimapped]}

Section page ›

Dictionary word

matrix format

matrix_format · Sequencing pack

Kind: format
Spelled: mtx, h5ad, loom, rds_matrix, anndata

As YAML for a pack file

  - {term: matrix_format, theme_kind: format, surfaces: [mtx, h5ad, loom, rds_matrix, anndata]}

Section page ›

Dictionary word

metagenomics

metagenomics · Sequencing pack

Kind: technique
Spelled: metagenome, metagenomics, 16s, its, shotgun_meta, amplicon_16s

As YAML for a pack file

  - {term: metagenomics, theme_kind: technique, surfaces: [metagenome, metagenomics, "16s", its,
     shotgun_meta, amplicon_16s]}

Section page ›

Dictionary word

methylation

methylation · Sequencing pack

Kind: technique
Spelled: methylseq, bisulfite, wgbs, rrbs, emseq, methylation_array

As YAML for a pack file

  - {term: methylation, theme_kind: technique, surfaces: [methylseq, bisulfite, wgbs, rrbs,
     emseq, methylation_array]}

Section page ›

Dictionary word

multiple alignment format

multiple_alignment_format · Sequencing pack

Kind: format
Spelled: aln, msa, sto, stockholm

As YAML for a pack file

  - {term: multiple_alignment_format, theme_kind: format, surfaces: [aln, msa, sto, stockholm]}

Section page ›

Dictionary word

normalised expression

normalised_expression · Sequencing pack

Kind: statistic
Spelled: tpm, fpkm, rpkm, cpm, vst, rlog, deseq_norm

As YAML for a pack file

  - {term: normalised_expression, theme_kind: statistic, surfaces: [tpm, fpkm, rpkm, cpm, vst,
     rlog, deseq_norm]}

Section page ›

Dictionary word

other platform

other_platform · Sequencing pack

Kind: instrument
Spelled: iontorrent, ion-torrent, bgi, mgi, element_bio, ultima

As YAML for a pack file

  - {term: other_platform, theme_kind: instrument, surfaces: [iontorrent, "ion-torrent", bgi,
     mgi, element_bio, ultima]}

Section page ›

Dictionary word

paired end

paired_end · Sequencing pack

Kind: read structure
Spelled: pe, paired, pairedend, paired-end

As YAML for a pack file

  - {term: paired_end, theme_kind: read_structure, surfaces: [pe, paired, pairedend,
     "paired-end"]}

Section page ›

Dictionary word

peak calling

peak_calling · Sequencing pack

Kind: technique
Spelled: peaks, macs, macs2, macs3, seacr, homer_peaks, genrich

As YAML for a pack file

  - {term: peak_calling, theme_kind: technique, surfaces: [peaks, macs, macs2, macs3, seacr,
     homer_peaks, genrich]}

Section page ›

Dictionary word

provider sequence text

sequence_text · Sequencing pack

Kind: format
Spelled: seq

As YAML for a pack file

  - {term: sequence_text, canonical: "provider sequence text", theme_kind: format,
     surfaces: [seq], extension_only: [seq]}

Section page ›

Dictionary word

quality control

quality_control · Sequencing pack

Kind: technique
Spelled: fastqc, multiqc, qc_report, qualimap, picard_metrics

As YAML for a pack file

  - {term: quality_control, theme_kind: technique, surfaces: [fastqc, multiqc, qc_report,
     qualimap, picard_metrics]}

Section page ›

Dictionary word

quality score

quality_score · Sequencing pack

Kind: statistic
Spelled: phred, q20, q30, mapq, basequality

As YAML for a pack file

  - {term: quality_score, theme_kind: statistic, surfaces: [phred, q20, q30, mapq, basequality]}

Section page ›

Dictionary word

quantification tool

quantification_tool · Sequencing pack

Kind: technique
Spelled: featurecounts, htseq, rsem, stringtie, cufflinks

As YAML for a pack file

  - {term: quantification_tool, theme_kind: technique, surfaces: [featurecounts, htseq, rsem,
     stringtie, cufflinks]}

Section page ›

Dictionary word

read count

read_count · Sequencing pack

Kind: statistic
Spelled: readcount, rawcounts, countmatrix

As YAML for a pack file

  - {term: read_count, theme_kind: statistic, surfaces: [readcount, rawcounts, countmatrix]}

Section page ›

Dictionary word

read format

read_format · Sequencing pack

Kind: format
Spelled: fastq, fq, fasta, fa, fna, faa, fsa, sra

As YAML for a pack file

  - {term: read_format, theme_kind: format, surfaces: [fastq, fq, fasta, fa, fna, faa, fsa,
     sra]}

Section page ›

Dictionary word

read one

read_one · Sequencing pack

Kind: read structure
Spelled: _1, read1, forward, fwd

As YAML for a pack file

  - {term: read_one, theme_kind: read_structure, surfaces: [_1, read1, forward, fwd]}

Section page ›

Dictionary word

read one

read_one · Sequencing pack

Kind: read structure
Spelled: r1

As YAML for a pack file

  - {term: read_one, theme_kind: read_structure, surfaces: [r1], file_type: read_format}

Section page ›

Dictionary word

read two

read_two · Sequencing pack

Kind: read structure
Spelled: _2, read2, reverse, rev_read

As YAML for a pack file

  - {term: read_two, theme_kind: read_structure, surfaces: [_2, read2, reverse, rev_read]}

Section page ›

Dictionary word

read two

read_two · Sequencing pack

Kind: read structure
Spelled: r2

As YAML for a pack file

  - {term: read_two, theme_kind: read_structure, surfaces: [r2], file_type: read_format}

Section page ›

Dictionary word

ribosome profiling

ribosome_profiling · Sequencing pack

Kind: technique
Spelled: riboseq, ribo-seq, tracking_ribosome

As YAML for a pack file

  - {term: ribosome_profiling, theme_kind: technique, surfaces: [riboseq, "ribo-seq",
     tracking_ribosome]}

Section page ›

Dictionary word

rna sequencing

rna_sequencing · Sequencing pack

Kind: technique
Spelled: rnaseq, rna-seq, mrnaseq, totalrna, polya_seq

As YAML for a pack file

  - {term: rna_sequencing, theme_kind: technique, surfaces: [rnaseq, "rna-seq", mrnaseq,
     totalrna, polya_seq]}

Section page ›

Dictionary word

short read platform

short_read_platform · Sequencing pack

Kind: instrument
Spelled: illumina, miseq, nextseq, novaseq, hiseq, iseq, nextera

As YAML for a pack file

  - {term: short_read_platform, theme_kind: instrument, surfaces: [illumina, miseq, nextseq,
     novaseq, hiseq, iseq, nextera]}

Section page ›

Dictionary word

single cell rna

single_cell_rna · Sequencing pack

Kind: technique
Spelled: scrnaseq, sc-rna-seq, snrnaseq, single-cell rna sequencing, single-cell rna-seq, single-cell transcriptomics, tenx, 10x and 2 more

As YAML for a pack file

  - {term: single_cell_rna, theme_kind: technique, surfaces: [scrnaseq, "sc-rna-seq", snrnaseq,
     "single-cell rna sequencing", "single-cell rna-seq", "single-cell transcriptomics", tenx, "10x",
     dropseq, smartseq]}

Section page ›

Dictionary word

single end

single_end · Sequencing pack

Kind: read structure
Spelled: se, singleend, single-end

As YAML for a pack file

  - {term: single_end, theme_kind: read_structure, surfaces: [se, singleend, "single-end"]}

Section page ›

Dictionary word

spatial transcriptomics

spatial_transcriptomics · Sequencing pack

Kind: technique
Spelled: spatial, visium, merfish, seqfish, xenium_class, slideseq

As YAML for a pack file

  - {term: spatial_transcriptomics, theme_kind: technique, surfaces: [spatial, visium, merfish,
     seqfish, xenium_class, slideseq]}

Section page ›

Dictionary word

trimming

trimming · Sequencing pack

Kind: technique
Spelled: trim, trimmed, trimmomatic, cutadapt, fastp, adapterremoval, clipped

As YAML for a pack file

  - {term: trimming, theme_kind: technique, surfaces: [trim, trimmed, trimmomatic, cutadapt,
     fastp, adapterremoval, clipped]}

Section page ›

Dictionary word

variant calling

variant_calling · Sequencing pack

Kind: technique
Spelled: variants, gatk, freebayes, bcftools_call, mutect, strelka, deepvariant, haplotypecaller

As YAML for a pack file

  - {term: variant_calling, theme_kind: technique, surfaces: [variants, gatk, freebayes,
     bcftools_call, mutect, strelka, deepvariant, haplotypecaller]}

Section page ›

Dictionary word

variant format

variant_format · Sequencing pack

Kind: format
Spelled: vcf, bcf, gvcf, maf

As YAML for a pack file

  - {term: variant_format, theme_kind: format, surfaces: [vcf, bcf, gvcf, maf]}

Section page ›

Spectrometry pack 22 words

Mass spectrometry, optical and magnetic spectroscopy, and their measures. Version 3. A project loads a pack by name. Pack page

Word	Kind	Means	Pack
absorbance spectroscopy	technique	Spelled `uv`, `vis`, `uvvis`, `uv-vis`, `absorbance` and 4 more	Spectrometry pack
acquisition mode	technique	Spelled `dda`, `dia`, `swath`, `prm`, `srm` and 3 more	Spectrometry pack
analyser	instrument	Spelled `tof`, `qtof`, `orbitrap`, `quadrupole`, `iontrap` and 3 more	Spectrometry pack
chiroptical	technique	Spelled `cd_spec`, `circulardichroism`, `circular-dichroism`, `ord`	Spectrometry pack
crystallography	technique	Spelled `xrd`, `crystallography`, `diffraction`, `x-ray crystallography`, `x-ray diffraction` and 5 more	Spectrometry pack
fluorescence spectroscopy	technique	Spelled `emission_spectrum`, `excitation_spectrum`, `spectralscan`, `lambda_scan`, `anisotropy` and 1 more	Spectrometry pack
ionisation	technique	Spelled `esi`, `maldi`, `apci`, `appi`, `nanospray` and 2 more	Spectrometry pack
labelling strategy	technique	Spelled `tmt`, `itraq`, `silac`, `dimethyl_label`, `labelfree` and 2 more	Spectrometry pack
mass spectrometry	technique	Spelled `massspec`, `mass-spec`, `lcms`, `lc-ms`, `gcms` and 7 more	Spectrometry pack
modification	technique	Spelled `ptm`, `phospho`, `phosphorylation`, `acetyl`, `methyl` and 5 more	Spectrometry pack
ms format	format	Spelled `raw_ms`, `mzml`, `mzxml`, `mgf`, `mzid` and 4 more	Spectrometry pack
ms measure	statistic	Spelled `mz`, `m/z`, `precursor`, `fragment_ion`, `retentiontime` and 7 more	Spectrometry pack
nmr experiment	technique	Spelled `cosy`, `hsqc`, `hmbc`, `noesy`, `roesy` and 3 more	Spectrometry pack
nmr measure	statistic	Spelled `chemicalshift`, `chemical-shift`, `ppm_shift`, `coupling_constant`, `jcoupling` and 2 more	Spectrometry pack
nuclear magnetic resonance	technique	Spelled `nmr`, `hnmr`, `1h-nmr`, `cnmr`, `13c-nmr` and 2 more	Spectrometry pack
omics application	technique	Spelled `proteomics`, `metabolomics`, `lipidomics`, `glycomics`, `peptidomics`	Spectrometry pack
plate reader protocol (Gen5) `plate_reader_protocol`	format	Spelled `prt`	Spectrometry pack
rheology	technique	Spelled `rheology`, `rheometry`	Spectrometry pack
scattering	technique	Spelled `dls`, `sls`, `saxs`, `waxs`, `sans` and 2 more	Spectrometry pack
search engine	software	Spelled `mascot`, `maxquant`, `proteomediscoverer`, `fragpipe`, `msfragger` and 5 more	Spectrometry pack
thermal analysis	technique	Spelled `dsc`, `itc`, `tga`, `thermalshift`, `tsa` and 2 more	Spectrometry pack
vibrational spectroscopy	technique	Spelled `ir`, `ftir`, `raman`, `atr`, `nearinfrared` and 1 more	Spectrometry pack

Dictionary word

absorbance spectroscopy

absorbance_spectroscopy · Spectrometry pack

Kind: technique
Spelled: uv, vis, uvvis, uv-vis, absorbance, od, od600, a280_spec and 1 more

As YAML for a pack file

  - {term: absorbance_spectroscopy, theme_kind: technique, surfaces: [uv, vis, uvvis, "uv-vis",
     absorbance, od, od600, a280_spec, a260_spec]}

Section page ›

Dictionary word

acquisition mode

acquisition_mode · Spectrometry pack

Kind: technique
Spelled: dda, dia, swath, prm, srm, mrm, targeted_ms, untargeted

As YAML for a pack file

  - {term: acquisition_mode, theme_kind: technique, surfaces: [dda, dia, swath, prm, srm, mrm,
     targeted_ms, untargeted]}

Section page ›

Dictionary word

analyser

analyser · Spectrometry pack

Kind: instrument
Spelled: tof, qtof, orbitrap, quadrupole, iontrap, ftms, triplequad, qqq

As YAML for a pack file

  - {term: analyser, theme_kind: instrument, surfaces: [tof, qtof, orbitrap, quadrupole, iontrap,
     ftms, triplequad, qqq]}

Section page ›

Dictionary word

chiroptical

chiroptical · Spectrometry pack

Kind: technique
Spelled: cd_spec, circulardichroism, circular-dichroism, ord

As YAML for a pack file

  - {term: chiroptical, theme_kind: technique, surfaces: [cd_spec, circulardichroism,
     "circular-dichroism", ord]}

Section page ›

Dictionary word

crystallography

crystallography · Spectrometry pack

Kind: technique
Spelled: xrd, crystallography, diffraction, x-ray crystallography, x-ray diffraction, unitcell, spacegroup, mtz and 2 more

As YAML for a pack file

  - {term: crystallography, theme_kind: technique, surfaces: [xrd, crystallography, diffraction,
     "x-ray crystallography", "x-ray diffraction", unitcell, spacegroup, mtz, pdb_file, cif]}

Section page ›

Dictionary word

fluorescence spectroscopy

fluorescence_spectroscopy · Spectrometry pack

Kind: technique
Spelled: emission_spectrum, excitation_spectrum, spectralscan, lambda_scan, anisotropy, polarisation_spec

As YAML for a pack file

  - {term: fluorescence_spectroscopy, theme_kind: technique, surfaces: [emission_spectrum,
     excitation_spectrum, spectralscan, lambda_scan, anisotropy, polarisation_spec]}

Section page ›

Dictionary word

ionisation

ionisation · Spectrometry pack

Kind: technique
Spelled: esi, maldi, apci, appi, nanospray, ei_ionisation, ci_ionisation

As YAML for a pack file

  - {term: ionisation, theme_kind: technique, surfaces: [esi, maldi, apci, appi, nanospray,
     ei_ionisation, ci_ionisation]}

Section page ›

Dictionary word

labelling strategy

labelling_strategy · Spectrometry pack

Kind: technique
Spelled: tmt, itraq, silac, dimethyl_label, labelfree, label-free, spikein

As YAML for a pack file

  - {term: labelling_strategy, theme_kind: technique, surfaces: [tmt, itraq, silac,
     dimethyl_label, labelfree, "label-free", spikein]}

Section page ›

Dictionary word

mass spectrometry

mass_spectrometry · Spectrometry pack

Kind: technique
Spelled: massspec, mass-spec, lcms, lc-ms, gcms, gc-ms, lcmsms, msms and 4 more

As YAML for a pack file

  - {term: mass_spectrometry, theme_kind: technique, surfaces: [massspec, "mass-spec", lcms,
     "lc-ms", gcms, "gc-ms", lcmsms, msms, "ms/ms", ms1, ms2, ms3]}

Section page ›

Dictionary word

modification

modification · Spectrometry pack

Kind: technique
Spelled: ptm, phospho, phosphorylation, acetyl, methyl, ubiquitin, glyco, sumo and 2 more

As YAML for a pack file

  - {term: modification, theme_kind: technique, surfaces: [ptm, phospho, phosphorylation, acetyl,
     methyl, ubiquitin, glyco, sumo, oxidation, carbamidomethyl]}

Section page ›

Dictionary word

ms format

ms_format · Spectrometry pack

Kind: format
Spelled: raw_ms, mzml, mzxml, mgf, mzid, wiff, d_folder, pepxml and 1 more

As YAML for a pack file

  - {term: ms_format, theme_kind: format, surfaces: [raw_ms, mzml, mzxml, mgf, mzid, wiff,
     d_folder, pepxml, protxml]}

Section page ›

Dictionary word

ms measure

ms_measure · Spectrometry pack

Kind: statistic
Spelled: mz, m/z, precursor, fragment_ion, retentiontime, retention-time, rt_ms, peakarea and 4 more

As YAML for a pack file

  - {term: ms_measure, theme_kind: statistic, surfaces: [mz, "m/z", precursor, fragment_ion,
     retentiontime, "retention-time", rt_ms, peakarea, peakheight, intensity_ms, isotope,
     charge_state]}

Section page ›

Dictionary word

nmr experiment

nmr_experiment · Spectrometry pack

Kind: technique
Spelled: cosy, hsqc, hmbc, noesy, roesy, tocsy, dept, hetcor

As YAML for a pack file

  - {term: nmr_experiment, theme_kind: technique, surfaces: [cosy, hsqc, hmbc, noesy, roesy,
     tocsy, dept, hetcor]}

Section page ›

Dictionary word

nmr measure

nmr_measure · Spectrometry pack

Kind: statistic
Spelled: chemicalshift, chemical-shift, ppm_shift, coupling_constant, jcoupling, multiplet, integration_nmr

As YAML for a pack file

  - {term: nmr_measure, theme_kind: statistic, surfaces: [chemicalshift, "chemical-shift",
     ppm_shift, coupling_constant, jcoupling, multiplet, integration_nmr]}

Section page ›

Dictionary word

nuclear magnetic resonance

nuclear_magnetic_resonance · Spectrometry pack

Kind: technique
Spelled: nmr, hnmr, 1h-nmr, cnmr, 13c-nmr, pnmr, fnmr

As YAML for a pack file

  - {term: nuclear_magnetic_resonance, theme_kind: technique, surfaces: [nmr, hnmr, "1h-nmr",
     cnmr, "13c-nmr", pnmr, fnmr]}

Section page ›

Dictionary word

omics application

omics_application · Spectrometry pack

Kind: technique
Spelled: proteomics, metabolomics, lipidomics, glycomics, peptidomics

As YAML for a pack file

  - {term: omics_application, theme_kind: technique, surfaces: [proteomics, metabolomics,
     lipidomics, glycomics, peptidomics]}

Section page ›

Dictionary word

plate reader protocol (Gen5)

plate_reader_protocol · Spectrometry pack

Kind: format
Spelled: prt

As YAML for a pack file

  - {term: plate_reader_protocol, canonical: "plate reader protocol (Gen5)", theme_kind: format,
     surfaces: [prt], extension_only: true, origins: {prt: {vendor: "Agilent BioTek Gen5",
     written_by: software}}}

Section page ›

Dictionary word

rheology

rheology · Spectrometry pack

Kind: technique
Spelled: rheology, rheometry

As YAML for a pack file

  - {term: rheology, theme_kind: technique, surfaces: [rheology, rheometry]}

Section page ›

Dictionary word

scattering

scattering · Spectrometry pack

Kind: technique
Spelled: dls, sls, saxs, waxs, sans, lightscattering, zeta_potential

As YAML for a pack file

  - {term: scattering, theme_kind: technique, surfaces: [dls, sls, saxs, waxs, sans,
     lightscattering, zeta_potential]}

Section page ›

Dictionary word

search engine

search_engine · Spectrometry pack

Kind: software
Spelled: mascot, maxquant, proteomediscoverer, fragpipe, msfragger, comet, sequest, skyline and 2 more

As YAML for a pack file

  - {term: search_engine, theme_kind: software, surfaces: [mascot, maxquant, proteomediscoverer,
     fragpipe, msfragger, comet, sequest, skyline, spectronaut, diann]}

Section page ›

Dictionary word

thermal analysis

thermal_analysis · Spectrometry pack

Kind: technique
Spelled: dsc, itc, tga, thermalshift, tsa, meltcurve, tm_value

As YAML for a pack file

  - {term: thermal_analysis, theme_kind: technique, surfaces: [dsc, itc, tga, thermalshift, tsa,
     meltcurve, tm_value]}

Section page ›

Dictionary word

vibrational spectroscopy

vibrational_spectroscopy · Spectrometry pack

Kind: technique
Spelled: ir, ftir, raman, atr, nearinfrared, nir

As YAML for a pack file

  - {term: vibrational_spectroscopy, theme_kind: technique, surfaces: [ir, ftir, raman, atr,
     nearinfrared, nir]}

Section page ›

Electrophysiology pack 19 words

Recording configurations, protocols, measured quantities and formats. Version 2. A project loads a pack by name. Pack page

Word	Kind	Means	Pack
access	measurement	Spelled `ra`, `rs`, `seriesresistance`, `series-resistance`, `accessresistance` and 3 more	Electrophysiology pack
action potential	measurement	Spelled `ap`, `actionpotential`, `action-potential`, `spike`, `spikes` and 6 more	Electrophysiology pack
array recording	technique	Spelled `mea`, `multi-electrode-array`, `multielectrode`, `hdmea`, `grid_array`	Electrophysiology pack
capacitance measure	measurement	Spelled `cm`, `membranecapacitance`, `wholecellcap`	Electrophysiology pack
clamp mode	technique	Spelled `voltageclamp`, `voltage-clamp`, `vc`, `currentclamp`, `current-clamp` and 3 more	Electrophysiology pack
ephys format	format	Spelled `abf`, `atf`, `wcp`, `ibw`, `smr` and 5 more	Electrophysiology pack
ephys software	software	Spelled `clampex`, `clampfit`, `pclamp`, `axograph`, `igor` and 5 more	Electrophysiology pack
extracellular	technique	Spelled `extracellular`, `lfp`, `local-field-potential`, `mua`, `sua` and 4 more	Electrophysiology pack
holding	measurement	Spelled `holding`, `holdingpotential`, `vhold`, `ihold`, `restingpotential` and 1 more	Electrophysiology pack
input resistance	measurement	Spelled `rin`, `inputresistance`, `input-resistance`	Electrophysiology pack
kinetics	measurement	Spelled `risetime`, `rise-time`, `decaytime`, `decay-time`, `tau` and 3 more	Electrophysiology pack
leak	measurement	Spelled `leak`, `leaksubtraction`, `leak-subtracted`, `pn_subtraction`	Electrophysiology pack
patch clamp	technique	Spelled `patch`, `patchclamp`, `patch-clamp`, `wholecell`, `whole-cell` and 5 more	Electrophysiology pack
plasticity	measurement	Spelled `ltp`, `ltd`, `stp`, `ppr`, `paired-pulse-ratio` and 2 more	Electrophysiology pack
protocol step	acquisition	Spelled `sweep`, `sweeps`, `episode`, `trace`, `traces` and 7 more	Electrophysiology pack
stimulation	technique	Spelled `stim`, `stimulation`, `stimulus`, `pulse_train`, `paired_pulse` and 4 more	Electrophysiology pack
surface recording	technique	Spelled `eeg`, `ecog`, `emg`, `ecg`, `ekg` and 1 more	Electrophysiology pack
synaptic current	measurement	Spelled `epsc`, `ipsc`, `mepsc`, `mipsc`, `sepsc` and 5 more	Electrophysiology pack
synaptic potential	measurement	Spelled `epsp`, `ipsp`, `psp`	Electrophysiology pack

Dictionary word

access

access · Electrophysiology pack

Kind: measurement
Spelled: ra, rs, seriesresistance, series-resistance, accessresistance, gigaseal, sealtest, sealresistance

As YAML for a pack file

  - {term: access, theme_kind: measurement, surfaces: [ra, rs, seriesresistance,
     "series-resistance", accessresistance, gigaseal, sealtest, sealresistance]}

Section page ›

Dictionary word

action potential

action_potential · Electrophysiology pack

Kind: measurement
Spelled: ap, actionpotential, action-potential, spike, spikes, firing, firingrate, burst and 3 more

As YAML for a pack file

  - {term: action_potential, theme_kind: measurement, surfaces: [ap, actionpotential,
     "action-potential", spike, spikes, firing, firingrate, burst, bursting, isi,
     "inter-spike-interval"]}

Section page ›

Dictionary word

array recording

array_recording · Electrophysiology pack

Kind: technique
Spelled: mea, multi-electrode-array, multielectrode, hdmea, grid_array

As YAML for a pack file

  - {term: array_recording, theme_kind: technique, surfaces: [mea, "multi-electrode-array",
     multielectrode, hdmea, grid_array]}

Section page ›

Dictionary word

capacitance measure

capacitance_measure · Electrophysiology pack

Kind: measurement
Spelled: cm, membranecapacitance, wholecellcap

As YAML for a pack file

  - {term: capacitance_measure, theme_kind: measurement, surfaces: [cm, membranecapacitance,
     wholecellcap]}

Section page ›

Dictionary word

clamp mode

clamp_mode · Electrophysiology pack

Kind: technique
Spelled: voltageclamp, voltage-clamp, vc, currentclamp, current-clamp, cc, iclamp, vclamp

As YAML for a pack file

  - {term: clamp_mode, theme_kind: technique, surfaces: [voltageclamp, "voltage-clamp", vc,
     currentclamp, "current-clamp", cc, iclamp, vclamp]}

Section page ›

Dictionary word

ephys format

ephys_format · Electrophysiology pack

Kind: format
Spelled: abf, atf, wcp, ibw, smr, nev, ns5, plx and 2 more

As YAML for a pack file

  - {term: ephys_format, theme_kind: format, surfaces: [abf, atf, wcp, ibw, smr, nev, ns5, plx,
     nwb, dat_ephys]}

Section page ›

Dictionary word

ephys software

ephys_software · Electrophysiology pack

Kind: software
Spelled: clampex, clampfit, pclamp, axograph, igor, spike2, plexon, kilosort and 2 more

As YAML for a pack file

  - {term: ephys_software, theme_kind: software, surfaces: [clampex, clampfit, pclamp, axograph,
     igor, spike2, plexon, kilosort, phy, mountainsort]}

Section page ›

Dictionary word

extracellular

extracellular · Electrophysiology pack

Kind: technique
Spelled: extracellular, lfp, local-field-potential, mua, sua, spikesorting, tetrode, silicon_probe and 1 more

As YAML for a pack file

  - {term: extracellular, theme_kind: technique, surfaces: [extracellular, lfp,
     "local-field-potential", mua, sua, spikesorting, tetrode, silicon_probe, neuropixels_class]}

Section page ›

Dictionary word

holding

holding · Electrophysiology pack

Kind: measurement
Spelled: holding, holdingpotential, vhold, ihold, restingpotential, vrest

As YAML for a pack file

  - {term: holding, theme_kind: measurement, surfaces: [holding, holdingpotential, vhold, ihold,
     restingpotential, vrest]}

Section page ›

Dictionary word

input resistance

input_resistance · Electrophysiology pack

Kind: measurement
Spelled: rin, inputresistance, input-resistance

As YAML for a pack file

  - {term: input_resistance, theme_kind: measurement, surfaces: [rin, inputresistance,
     "input-resistance"]}

Section page ›

Dictionary word

kinetics

kinetics · Electrophysiology pack

Kind: measurement
Spelled: risetime, rise-time, decaytime, decay-time, tau, halfwidth, amplitude_ephys, latency

As YAML for a pack file

  - {term: kinetics, theme_kind: measurement, surfaces: [risetime, "rise-time", decaytime,
     "decay-time", tau, halfwidth, amplitude_ephys, latency]}

Section page ›

Dictionary word

leak

leak · Electrophysiology pack

Kind: measurement
Spelled: leak, leaksubtraction, leak-subtracted, pn_subtraction

As YAML for a pack file

  - {term: leak, theme_kind: measurement, surfaces: [leak, leaksubtraction, "leak-subtracted",
     pn_subtraction]}

Section page ›

Dictionary word

patch clamp

patch_clamp · Electrophysiology pack

Kind: technique
Spelled: patch, patchclamp, patch-clamp, wholecell, whole-cell, cellattached, cell-attached, insideout and 2 more

As YAML for a pack file

  - {term: patch_clamp, theme_kind: technique, surfaces: [patch, patchclamp, "patch-clamp",
     wholecell, "whole-cell", cellattached, "cell-attached", insideout, outsideout, perforated]}

Section page ›

Dictionary word

plasticity

plasticity · Electrophysiology pack

Kind: measurement
Spelled: ltp, ltd, stp, ppr, paired-pulse-ratio, facilitation, depression_synaptic

As YAML for a pack file

  - {term: plasticity, theme_kind: measurement, surfaces: [ltp, ltd, stp, ppr,
     "paired-pulse-ratio", facilitation, depression_synaptic]}

Section page ›

Dictionary word

protocol step

protocol_step · Electrophysiology pack

Kind: acquisition
Spelled: sweep, sweeps, episode, trace, traces, sweep segment, protocol segment, run_protocol and 4 more

As YAML for a pack file

  - {term: protocol_step, theme_kind: acquisition, surfaces: [sweep, sweeps, episode, trace,
     traces, "sweep segment", "protocol segment", run_protocol, ramp, step_protocol, iv_protocol,
     "i-v"]}

Section page ›

Dictionary word

stimulation

stimulation · Electrophysiology pack

Kind: technique
Spelled: stim, stimulation, stimulus, pulse_train, paired_pulse, tetanus, optogenetic, chr2_class and 1 more

As YAML for a pack file

  - {term: stimulation, theme_kind: technique, surfaces: [stim, stimulation, stimulus,
     pulse_train, paired_pulse, tetanus, optogenetic, chr2_class, dbs]}

Section page ›

Dictionary word

surface recording

surface_recording · Electrophysiology pack

Kind: technique
Spelled: eeg, ecog, emg, ecg, ekg, meg

As YAML for a pack file

  - {term: surface_recording, theme_kind: technique, surfaces: [eeg, ecog, emg, ecg, ekg, meg]}

Section page ›

Dictionary word

synaptic current

synaptic_current · Electrophysiology pack

Kind: measurement
Spelled: epsc, ipsc, mepsc, mipsc, sepsc, sipsc, psc, evoked and 2 more

As YAML for a pack file

  - {term: synaptic_current, theme_kind: measurement, surfaces: [epsc, ipsc, mepsc, mipsc, sepsc,
     sipsc, psc, evoked, spontaneous, miniature]}

Section page ›

Dictionary word

synaptic potential

synaptic_potential · Electrophysiology pack

Kind: measurement
Spelled: epsp, ipsp, psp

As YAML for a pack file

  - {term: synaptic_potential, theme_kind: measurement, surfaces: [epsp, ipsp, psp]}

Section page ›

Biochemistry pack 121 words

Wet-laboratory techniques, reagent classes, cell culture and genetics. Version 3. A project loads a pack by name. Pack page

Word	Kind	Means	Pack
activator	reagent	Spelled `activator`, `agonist`, `stimulant`, `inducer_chem`	Biochemistry pack
ApE plasmid `ape_plasmid`	format	Spelled `ape`	Biochemistry pack
Arabidopsis thaliana `arabidopsis_thaliana`	subject	Spelled `arabidopsis thaliana`, `a thaliana`, `arabidopsis`, `thale cress`	Biochemistry pack
ATP-gamma-S `atp_gamma_s`	reagent	Spelled `atp gamma s`, `atpgammas`, `atpgs`, `atp gs`	Biochemistry pack
Bacillus subtilis `bacillus_subtilis`	subject	Spelled `bacillus subtilis`, `b subtilis`, `subtilis`	Biochemistry pack
BiP `bip`	subject	Spelled `bip`, `grp78`, `hspa5`, `grp 78`, `binding immunoglobulin protein`	Biochemistry pack
Bos taurus `bos_taurus`	subject	Spelled `bos taurus`, `b taurus`, `taurus`, `cattle`	Biochemistry pack
bovine serum albumin	reagent	Spelled `bsa`, `bovine serum albumin`	Biochemistry pack
buffer	reagent	Spelled `pbs`, `tbs`, `tbst`, `tris`, `hepes` and 9 more	Biochemistry pack
Caenorhabditis elegans `caenorhabditis_elegans`	subject	Spelled `caenorhabditis elegans`, `c elegans`, `elegans`	Biochemistry pack
calcium chloride	reagent	Spelled `cacl2`, `calcium chloride`	Biochemistry pack
calnexin	subject	Spelled `calnexin`, `canx`	Biochemistry pack
Caulobacter crescentus `caulobacter_crescentus`	subject	Spelled `caulobacter crescentus`, `c crescentus`, `caulobacter`, `crescentus`	Biochemistry pack
cell	subject	Spelled `cell`	Biochemistry pack
cell line generic	subject	Spelled `cellline`, `cell-line`, `line`, `clone`, `subclone` and 3 more	Biochemistry pack
Chlamydomonas reinhardtii `chlamydomonas_reinhardtii`	subject	Spelled `chlamydomonas reinhardtii`, `c reinhardtii`, `chlamydomonas`, `reinhardtii`	Biochemistry pack
CHO `cho`	subject	Spelled `chinese hamster ovary`, `cho cell`, `cho k1`	Biochemistry pack
cholecystokinin	reagent	Spelled `cholecystokinin`	Biochemistry pack
chromatogram ASCII export `chromatogram_export`	format	Spelled `asc`	Biochemistry pack
chromatography	technique	Spelled `hplc`, `uplc`, `fplc`, `gc`, `sec` and 3 more	Biochemistry pack
cloning	technique	Spelled `cloning`, `ligation`, `gibson`, `golden_gate`, `gateway` and 3 more	Biochemistry pack
CMV promoter `cmv_promoter`	reagent	Spelled `pcmv`, `cmv promoter`	Biochemistry pack
confluence	culture	Spelled `confluence`, `confluent`, `subconfluent`, `density_plated`, `seeded` and 1 more	Biochemistry pack
contamination check	culture	Spelled `mycoplasma`, `myco`, `sterility`, `str_profiling`, `authentication`	Biochemistry pack
COS-7 `cos7`	subject	Spelled `cos 7`, `cos7`	Biochemistry pack
cryopreservation	culture	Spelled `cryopreservation`, `cryopreserved`, `cryopreserve`, `cryoprotectant`, `cryoprotection` and 6 more	Biochemistry pack
cycloheximide	reagent	Spelled `cycloheximide`, `chx`	Biochemistry pack
Danio rerio `danio_rerio`	subject	Spelled `danio rerio`, `d rerio`, `zebrafish`	Biochemistry pack
delivery	technique	Spelled `transfection`, `transfected`, `transduction`, `transduced`, `electroporation` and 3 more	Biochemistry pack
dextran	reagent	Spelled `dextran`	Biochemistry pack
Dictyostelium discoideum `dictyostelium_discoideum`	subject	Spelled `dictyostelium discoideum`, `d discoideum`, `dictyostelium`, `discoideum`	Biochemistry pack
dimethyl sulfoxide	reagent	Spelled `dmso`, `dimethyl sulfoxide`, `dimethyl sulphoxide`, `dimethylsulfoxide`	Biochemistry pack
dissociation	culture	Spelled `trypsin`, `trypsinised`, `accutase`, `versene`, `edta_diss` and 1 more	Biochemistry pack
dithiothreitol	reagent	Spelled `dtt`, `dithiothreitol`	Biochemistry pack
dose response	condition	Spelled `doseresponse`, `dose-response`, `titration`, `serialdilution`, `serial-dilution` and 1 more	Biochemistry pack
Drosophila melanogaster `drosophila_melanogaster`	subject	Spelled `drosophila melanogaster`, `d melanogaster`, `drosophila`, `fruit fly`	Biochemistry pack
electrophoresis	technique	Spelled `gel`, `gels`, `electrophoresis`, `sdspage`, `sds-page` and 4 more	Biochemistry pack
Escherichia coli `escherichia_coli`	subject	Spelled `escherichia coli`, `e coli`	Biochemistry pack
extraction	technique	Spelled `miniprep`, `midiprep`, `maxiprep`, `extraction`, `purification` and 4 more	Biochemistry pack
flow cytometry	technique	Spelled `facs`, `flow`, `cytometry`, `sorting`, `gating_strategy` and 1 more	Biochemistry pack
flow cytometry data `flow_cytometry_format`	format	Spelled `fcs`	Biochemistry pack
FlowJo workspace `flowjo_workspace`	format	Spelled `wsp`	Biochemistry pack
Gallus gallus `gallus_gallus`	subject	Spelled `gallus gallus`, `g gallus`, `chicken`	Biochemistry pack
genome editing	technique	Spelled `crispr`, `cas9`, `cas12`, `base_editing`, `prime_editing` and 5 more	Biochemistry pack
genotype generic	subject	Spelled `mutant`, `mut`, `variant_strain`, `heterozygous`, `het` and 4 more	Biochemistry pack
glutathione S-transferase `glutathione_s_transferase`	reagent	Spelled `gst`, `glutathione s transferase`	Biochemistry pack
GraphPad Prism project `prism_project`	format	Spelled `pzfx`, `prism`	Biochemistry pack
HEK293 `hek293`	subject	Spelled `hek 293`, `hek 293t`	Biochemistry pack
HeLa `hela`	subject	Spelled `hela`	Biochemistry pack
Helicobacter pylori `helicobacter_pylori`	subject	Spelled `helicobacter pylori`, `h pylori`, `pylori`	Biochemistry pack
His tag `his_tag`	reagent	Spelled `his6`, `6x his`, `6 his`, `his tag`, `polyhistidine tag` and 1 more	Biochemistry pack
histamine	reagent	Spelled `histamine`	Biochemistry pack
Homo sapiens `homo_sapiens`	subject	Spelled `homo sapiens`, `h sapiens`	Biochemistry pack
Image Lab multichannel scan `imagelab_scan`	format	Spelled `mscn`	Biochemistry pack
immunoassay	technique	Spelled `elisa`, `aliquot_elisa`, `sandwich_elisa`, `luminex`, `msd_assay` and 1 more	Biochemistry pack
immunoblot	technique	Spelled `western`, `western-blot`, `immunoblot`, `blot`, `wb`	Biochemistry pack
induction	reagent	Spelled `induced`, `induction`, `doxycycline`, `dox`, `iptg` and 5 more	Biochemistry pack
inhibitor	reagent	Spelled `inhibitor`, `inh`, `antagonist`, `blocker`	Biochemistry pack
insulin	reagent	Spelled `insulin`	Biochemistry pack
ionomycin	reagent	Spelled `ionomycin`	Biochemistry pack
KDEL `kdel`	reagent	Spelled `kdel`, `er retention signal`	Biochemistry pack
knockdown	technique	Spelled `kd`, `knockdown`, `knock-down`, `sirna`, `shrna` and 4 more	Biochemistry pack
knockin	technique	Spelled `ki`, `knockin`, `knock-in`, `tagged`, `endogenous_tag` and 1 more	Biochemistry pack
knockout	technique	Spelled `ko`, `knockout`, `knock-out`, `null_allele`, `deletion_strain`	Biochemistry pack
mass photometry data	format	Spelled `mpr`, `mp`, `dmp`	Biochemistry pack
medium	reagent	Spelled `media`, `medium`, `dmem`, `rpmi`, `mem` and 8 more	Biochemistry pack
microscopy prep	technique	Spelled `fixation`, `fixed`, `pfa`, `formaldehyde`, `methanol_fix` and 8 more	Biochemistry pack
model organism generic	subject	Spelled `invitro`, `in-vitro`, `invivo`, `in-vivo`, `insilico` and 1 more	Biochemistry pack
molecular structure `structure_format`	format	Spelled `pdb`, `cif`, `mmcif`, `ent`	Biochemistry pack
Mus musculus `mus_musculus`	subject	Spelled `mus musculus`, `m musculus`, `mouse`, `mice`, `murine`	Biochemistry pack
Myc tag `myc_tag`	reagent	Spelled `myc tag`	Biochemistry pack
Mycobacterium tuberculosis `mycobacterium_tuberculosis`	subject	Spelled `mycobacterium tuberculosis`, `m tuberculosis`	Biochemistry pack
Neurospora crassa `neurospora_crassa`	subject	Spelled `neurospora crassa`, `n crassa`, `neurospora`	Biochemistry pack
Nicotiana benthamiana `nicotiana_benthamiana`	subject	Spelled `nicotiana benthamiana`, `n benthamiana`, `benthamiana`	Biochemistry pack
nocodazole	reagent	Spelled `nocodazole`	Biochemistry pack
novobiocin	reagent	Spelled `novobiocin`	Biochemistry pack
nucleic blot	technique	Spelled `southern`, `northern`, `dotblot`, `slotblot`	Biochemistry pack
oligomycin	reagent	Spelled `oligomycin`	Biochemistry pack
oligonucleotide	reagent	Spelled `primer`, `primers`, `oligo`, `oligos`, `probe` and 2 more	Biochemistry pack
Oryzias latipes `oryzias_latipes`	subject	Spelled `oryzias latipes`, `o latipes`, `latipes`, `medaka`	Biochemistry pack
overexpression	technique	Spelled `oe`, `overexpression`, `over-expression`, `ectopic`, `induced_expression`	Biochemistry pack
passage	culture	Spelled `passage`, `p1`, `p2`, `p3`, `p4` and 3 more	Biochemistry pack
phase separation	subject	Spelled `phase separation`, `liquid-liquid phase separation`, `llps`	Biochemistry pack
plasma membrane	subject	Spelled `plasma membrane`	Biochemistry pack
Plasmodium falciparum `plasmodium_falciparum`	subject	Spelled `plasmodium falciparum`, `p falciparum`, `falciparum`	Biochemistry pack
plate imager experiment	format	Spelled `xpt`	Biochemistry pack
plate reader data	format	Spelled `pda`	Biochemistry pack
polyethylene glycol	reagent	Spelled `peg`, `peg4k`, `peg6k`, `peg8k`, `peg10k` and 8 more	Biochemistry pack
polymerase chain reaction	technique	Spelled `pcr`, `rtpcr`, `rt-pcr`, `qpcr`, `q-pcr` and 5 more	Biochemistry pack
potassium chloride	reagent	Spelled `kcl`, `potassium chloride`	Biochemistry pack
primary culture	subject	Spelled `primary`, `primaries`, `ipsc`, `esc`, `organoid` and 3 more	Biochemistry pack
proteinase K `proteinase_k`	reagent	Spelled `proteinase k`, `protk`	Biochemistry pack
PyMOL session `pymol_session`	format	Spelled `pse`	Biochemistry pack
quantitation	technique	Spelled `nanodrop`, `qubit`, `bioanalyzer`, `tapestation`, `a260` and 3 more	Biochemistry pack
Rattus norvegicus `rattus_norvegicus`	subject	Spelled `rattus norvegicus`, `r norvegicus`, `norvegicus`, `rat`	Biochemistry pack
restriction	technique	Spelled `digest`, `digestion`, `restriction`, `linearised`, `linearized` and 1 more	Biochemistry pack
Saccharomyces cerevisiae `saccharomyces_cerevisiae`	subject	Spelled `saccharomyces cerevisiae`, `s cerevisiae`, `cerevisiae`, `budding yeast`	Biochemistry pack
saponin	reagent	Spelled `saponin`	Biochemistry pack
Schizosaccharomyces pombe `schizosaccharomyces_pombe`	subject	Spelled `schizosaccharomyces pombe`, `s pombe`, `pombe`, `fission yeast`	Biochemistry pack
Schmidtea mediterranea `schmidtea_mediterranea`	subject	Spelled `schmidtea mediterranea`, `s mediterranea`, `schmidtea`	Biochemistry pack
selection	reagent	Spelled `selection`, `puromycin`, `blasticidin`, `hygromycin`, `neomycin` and 5 more	Biochemistry pack
SnapGene plasmid `snapgene_plasmid`	format	Spelled `dna`, `prot`, `clxn`	Biochemistry pack
sodium dodecyl sulfate	reagent	Spelled `sds`, `sodium dodecyl sulfate`, `sodium dodecyl sulphate`	Biochemistry pack
Staphylococcus aureus `staphylococcus_aureus`	subject	Spelled `staphylococcus aureus`, `s aureus`, `aureus`	Biochemistry pack
stress	condition	Spelled `heatshock`, `heat-shock`, `coldshock`, `oxidative`, `osmotic` and 3 more	Biochemistry pack
supplement	reagent	Spelled `fbs`, `fcs`, `serum`, `penstrep`, `pen-strep` and 6 more	Biochemistry pack
Tetrahymena thermophila `tetrahymena_thermophila`	subject	Spelled `tetrahymena thermophila`, `t thermophila`, `tetrahymena`, `thermophila`	Biochemistry pack
thapsigargin	reagent	Spelled `thapsigargin`	Biochemistry pack
Toxoplasma gondii `toxoplasma_gondii`	subject	Spelled `toxoplasma gondii`, `t gondii`, `toxoplasma`, `gondii`	Biochemistry pack
Triticum aestivum `triticum_aestivum`	subject	Spelled `triticum aestivum`, `t aestivum`, `aestivum`, `wheat`	Biochemistry pack
Trypanosoma brucei `trypanosoma_brucei`	subject	Spelled `trypanosoma brucei`, `t brucei`, `brucei`	Biochemistry pack
tunicamycin	reagent	Spelled `tunicamycin`	Biochemistry pack
Tween 20 `polysorbate_20`	reagent	Spelled `tween 20`, `polysorbate 20`	Biochemistry pack
U2OS `u2os`	subject	Spelled `u2os`, `u 2 os`, `u20s`	Biochemistry pack
UbC promoter `ubc_promoter`	reagent	Spelled `ubc promoter`, `ubiquitin c promoter`	Biochemistry pack
vector	reagent	Spelled `plasmid`, `vector`, `backbone`, `insert`, `construct` and 6 more	Biochemistry pack
viral vector	reagent	Spelled `lentivirus`, `lenti`, `retrovirus`, `aav`, `adenovirus` and 2 more	Biochemistry pack
washout	condition	Spelled `washout`, `wash-out`, `recovery_period`, `chase`, `pulse_chase`	Biochemistry pack
Xenopus laevis `xenopus_laevis`	subject	Spelled `xenopus laevis`, `x laevis`, `laevis`, `african clawed frog`	Biochemistry pack
Xenopus tropicalis `xenopus_tropicalis`	subject	Spelled `xenopus tropicalis`, `x tropicalis`, `tropicalis`, `western clawed frog`	Biochemistry pack
Zea mays `zea_mays`	subject	Spelled `zea mays`, `z mays`, `maize`	Biochemistry pack

Dictionary word

activator

activator · Biochemistry pack

Kind: reagent
Spelled: activator, agonist, stimulant, inducer_chem

As YAML for a pack file

  - {term: activator, theme_kind: reagent, surfaces: [activator, agonist, stimulant,
     inducer_chem]}

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Dictionary word

ApE plasmid

ape_plasmid · Biochemistry pack

Kind: format
Spelled: ape

As YAML for a pack file

  - {term: ape_plasmid, canonical: "ApE plasmid", theme_kind: format, surfaces: [ape],
     extension_only: [ape]}

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Dictionary word

Arabidopsis thaliana

arabidopsis_thaliana · Biochemistry pack

Kind: subject
Spelled: arabidopsis thaliana, a thaliana, arabidopsis, thale cress

As YAML for a pack file

  - {term: arabidopsis_thaliana, canonical: "Arabidopsis thaliana", theme_kind: subject,
     surfaces: ["arabidopsis thaliana", "a thaliana", arabidopsis, "thale cress"]}

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Dictionary word

ATP-gamma-S

atp_gamma_s · Biochemistry pack

Kind: reagent
Spelled: atp gamma s, atpgammas, atpgs, atp gs

As YAML for a pack file

  - {term: atp_gamma_s, canonical: "ATP-gamma-S", theme_kind: reagent, surfaces: ["atp gamma s",
     atpgammas, atpgs, "atp gs"], ontology_ids: ["ChEBI:27575", "PubChem:440317"]}

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Dictionary word

Bacillus subtilis

bacillus_subtilis · Biochemistry pack

Kind: subject
Spelled: bacillus subtilis, b subtilis, subtilis

As YAML for a pack file

  - {term: bacillus_subtilis, canonical: "Bacillus subtilis", theme_kind: subject,
     surfaces: ["bacillus subtilis", "b subtilis", subtilis]}

Section page ›

Dictionary word

BiP

bip · Biochemistry pack

Kind: subject
Spelled: bip, grp78, hspa5, grp 78, binding immunoglobulin protein

As YAML for a pack file

  - {term: bip, canonical: BiP, theme_kind: subject, surfaces: [bip, grp78, hspa5, "grp 78",
     "binding immunoglobulin protein"], ontology_ids: ["UniProt:P11021"]}

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Dictionary word

Bos taurus

bos_taurus · Biochemistry pack

Kind: subject
Spelled: bos taurus, b taurus, taurus, cattle

As YAML for a pack file

  - {term: bos_taurus, canonical: "Bos taurus", theme_kind: subject, surfaces: ["bos taurus",
     "b taurus", taurus, cattle]}

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Dictionary word

bovine serum albumin

bovine_serum_albumin · Biochemistry pack

Kind: reagent
Spelled: bsa, bovine serum albumin

As YAML for a pack file

  - {term: bovine_serum_albumin, canonical: "bovine serum albumin", theme_kind: reagent,
     surfaces: [bsa, "bovine serum albumin"], ontology_ids: ["UniProt:P02769"]}

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Dictionary word

buffer

buffer · Biochemistry pack

Kind: reagent
Spelled: pbs, tbs, tbst, tris, hepes, mops, mes, hbss and 6 more

As YAML for a pack file

  - {term: buffer, theme_kind: reagent, surfaces: [pbs, tbs, tbst, tris, hepes, mops, mes, hbss,
     tae, tbe, ripa, lysis_buffer, sample_buffer, laemmli]}

Section page ›

Dictionary word

Caenorhabditis elegans

caenorhabditis_elegans · Biochemistry pack

Kind: subject
Spelled: caenorhabditis elegans, c elegans, elegans

As YAML for a pack file

  - {term: caenorhabditis_elegans, canonical: "Caenorhabditis elegans", theme_kind: subject,
     surfaces: ["caenorhabditis elegans", "c elegans", elegans]}

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Dictionary word

calcium chloride

calcium_chloride · Biochemistry pack

Kind: reagent
Spelled: cacl2, calcium chloride

As YAML for a pack file

  - {term: calcium_chloride, canonical: "calcium chloride", theme_kind: reagent,
     surfaces: [cacl2, "calcium chloride"], ontology_ids: ["ChEBI:3312", "PubChem:5284359"]}

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Dictionary word

calnexin

calnexin · Biochemistry pack

Kind: subject
Spelled: calnexin, canx

As YAML for a pack file

  - {term: calnexin, theme_kind: subject, surfaces: [calnexin, canx],
     ontology_ids: ["UniProt:P27824"]}

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Dictionary word

Caulobacter crescentus

caulobacter_crescentus · Biochemistry pack

Kind: subject
Spelled: caulobacter crescentus, c crescentus, caulobacter, crescentus

As YAML for a pack file

  - {term: caulobacter_crescentus, canonical: "Caulobacter crescentus", theme_kind: subject,
     surfaces: ["caulobacter crescentus", "c crescentus", caulobacter, crescentus]}

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Dictionary word

cell

cell · Biochemistry pack

Kind: subject
Spelled: cell

As YAML for a pack file

  - {term: cell, theme_kind: subject, surfaces: [cell]}

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Dictionary word

cell line generic

cell_line_generic · Biochemistry pack

Kind: subject
Spelled: cellline, cell-line, line, clone, subclone, isolate, strain, background_strain

As YAML for a pack file

  - {term: cell_line_generic, theme_kind: subject, surfaces: [cellline, "cell-line", line, clone,
     subclone, isolate, strain, background_strain]}

Section page ›

Dictionary word

Chlamydomonas reinhardtii

chlamydomonas_reinhardtii · Biochemistry pack

Kind: subject
Spelled: chlamydomonas reinhardtii, c reinhardtii, chlamydomonas, reinhardtii

As YAML for a pack file

  - {term: chlamydomonas_reinhardtii, canonical: "Chlamydomonas reinhardtii",
     theme_kind: subject, surfaces: ["chlamydomonas reinhardtii", "c reinhardtii", chlamydomonas,
     reinhardtii]}

Section page ›

Dictionary word

CHO

cho · Biochemistry pack

Kind: subject
Spelled: chinese hamster ovary, cho cell, cho k1

As YAML for a pack file

  - {term: cho, canonical: CHO, theme_kind: subject, surfaces: ["chinese hamster ovary",
     "cho cell", "cho k1"], ontology_ids: ["Cellosaurus:CVCL_0213", "Cellosaurus:CVCL_0214"]}

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Dictionary word

cholecystokinin

cholecystokinin · Biochemistry pack

Kind: reagent
Spelled: cholecystokinin

As YAML for a pack file

  - {term: cholecystokinin, theme_kind: reagent, surfaces: [cholecystokinin],
     ontology_ids: ["UniProt:P06307"]}

Section page ›

Dictionary word

chromatogram ASCII export

chromatogram_export · Biochemistry pack

Kind: format
Spelled: asc

As YAML for a pack file

  - {term: chromatogram_export, canonical: "chromatogram ASCII export", theme_kind: format,
     surfaces: [asc], extension_only: [asc]}

Section page ›

Dictionary word

chromatography

chromatography · Biochemistry pack

Kind: technique
Spelled: hplc, uplc, fplc, gc, sec, iex, affinity_chrom, column

As YAML for a pack file

  - {term: chromatography, theme_kind: technique, surfaces: [hplc, uplc, fplc, gc, sec, iex,
     affinity_chrom, column]}

Section page ›

Dictionary word

cloning

cloning · Biochemistry pack

Kind: technique
Spelled: cloning, ligation, gibson, golden_gate, gateway, topo, infusion, assembly_cloning

As YAML for a pack file

  - {term: cloning, theme_kind: technique, surfaces: [cloning, ligation, gibson, golden_gate,
     gateway, topo, infusion, assembly_cloning]}

Section page ›

Dictionary word

CMV promoter

cmv_promoter · Biochemistry pack

Kind: reagent
Spelled: pcmv, cmv promoter

As YAML for a pack file

  - {term: cmv_promoter, canonical: "CMV promoter", theme_kind: reagent, surfaces: [pcmv,
     "cmv promoter"]}

Section page ›

Dictionary word

confluence

confluence · Biochemistry pack

Kind: culture
Spelled: confluence, confluent, subconfluent, density_plated, seeded, seeding

As YAML for a pack file

  - {term: confluence, theme_kind: culture, surfaces: [confluence, confluent, subconfluent,
     density_plated, seeded, seeding]}

Section page ›

Dictionary word

contamination check

contamination_check · Biochemistry pack

Kind: culture
Spelled: mycoplasma, myco, sterility, str_profiling, authentication

As YAML for a pack file

  - {term: contamination_check, theme_kind: culture, surfaces: [mycoplasma, myco, sterility,
     str_profiling, authentication]}

Section page ›

Dictionary word

COS-7

cos7 · Biochemistry pack

Kind: subject
Spelled: cos 7, cos7

As YAML for a pack file

  - {term: cos7, canonical: "COS-7", theme_kind: subject, surfaces: ["cos 7", cos7],
     ontology_ids: ["Cellosaurus:CVCL_0224"]}

Section page ›

Dictionary word

cryopreservation

cryopreservation · Biochemistry pack

Kind: culture
Spelled: cryopreservation, cryopreserved, cryopreserve, cryoprotectant, cryoprotection, cryovial, frozen_stock, thawed and 3 more

As YAML for a pack file

  - {term: cryopreservation, theme_kind: culture, surfaces: [cryopreservation, cryopreserved,
     cryopreserve, cryoprotectant, cryoprotection, cryovial, frozen_stock, thawed, dmso_freeze,
     ln2_stored, vial_stock]}

Section page ›

Dictionary word

cycloheximide

cycloheximide · Biochemistry pack

Kind: reagent
Spelled: cycloheximide, chx

As YAML for a pack file

  - {term: cycloheximide, theme_kind: reagent, surfaces: [cycloheximide, chx],
     ontology_ids: ["ChEBI:27641", "PubChem:6197"]}

Section page ›

Dictionary word

Danio rerio

danio_rerio · Biochemistry pack

Kind: subject
Spelled: danio rerio, d rerio, zebrafish

As YAML for a pack file

  - {term: danio_rerio, canonical: "Danio rerio", theme_kind: subject, surfaces: ["danio rerio",
     "d rerio", zebrafish]}

Section page ›

Dictionary word

delivery

delivery · Biochemistry pack

Kind: technique
Spelled: transfection, transfected, transduction, transduced, electroporation, nucleofection, lipofection, infection_viral

As YAML for a pack file

  - {term: delivery, theme_kind: technique, surfaces: [transfection, transfected, transduction,
     transduced, electroporation, nucleofection, lipofection, infection_viral]}

Section page ›

Dictionary word

dextran

dextran · Biochemistry pack

Kind: reagent
Spelled: dextran

As YAML for a pack file

  - {term: dextran, theme_kind: reagent, surfaces: [dextran], ontology_ids: ["ChEBI:52071"]}

Section page ›

Dictionary word

Dictyostelium discoideum

dictyostelium_discoideum · Biochemistry pack

Kind: subject
Spelled: dictyostelium discoideum, d discoideum, dictyostelium, discoideum

As YAML for a pack file

  - {term: dictyostelium_discoideum, canonical: "Dictyostelium discoideum", theme_kind: subject,
     surfaces: ["dictyostelium discoideum", "d discoideum", dictyostelium, discoideum]}

Section page ›

Dictionary word

dimethyl sulfoxide

dimethyl_sulfoxide · Biochemistry pack

Kind: reagent
Spelled: dmso, dimethyl sulfoxide, dimethyl sulphoxide, dimethylsulfoxide

As YAML for a pack file

  - {term: dimethyl_sulfoxide, canonical: "dimethyl sulfoxide", theme_kind: reagent,
     surfaces: [dmso, "dimethyl sulfoxide", "dimethyl sulphoxide", dimethylsulfoxide],
     ontology_ids: ["ChEBI:28262", "PubChem:679"]}

Section page ›

Dictionary word

dissociation

dissociation · Biochemistry pack

Kind: culture
Spelled: trypsin, trypsinised, accutase, versene, edta_diss, scraped

As YAML for a pack file

  - {term: dissociation, theme_kind: culture, surfaces: [trypsin, trypsinised, accutase, versene,
     edta_diss, scraped]}

Section page ›

Dictionary word

dithiothreitol

dithiothreitol · Biochemistry pack

Kind: reagent
Spelled: dtt, dithiothreitol

As YAML for a pack file

  - {term: dithiothreitol, theme_kind: reagent, surfaces: [dtt, dithiothreitol],
     ontology_ids: ["ChEBI:18320", "PubChem:439196"]}

Section page ›

Dictionary word

dose response

dose_response · Biochemistry pack

Kind: condition
Spelled: doseresponse, dose-response, titration, serialdilution, serial-dilution, curve_dose

As YAML for a pack file

  - {term: dose_response, theme_kind: condition, surfaces: [doseresponse, "dose-response",
     titration, serialdilution, "serial-dilution", curve_dose]}

Section page ›

Dictionary word

Drosophila melanogaster

drosophila_melanogaster · Biochemistry pack

Kind: subject
Spelled: drosophila melanogaster, d melanogaster, drosophila, fruit fly

As YAML for a pack file

  - {term: drosophila_melanogaster, canonical: "Drosophila melanogaster", theme_kind: subject,
     surfaces: ["drosophila melanogaster", "d melanogaster", drosophila, "fruit fly"]}

Section page ›

Dictionary word

electrophoresis

electrophoresis · Biochemistry pack

Kind: technique
Spelled: gel, gels, electrophoresis, sdspage, sds-page, page_gel, agarose_gel, nativegel and 1 more

As YAML for a pack file

  - {term: electrophoresis, theme_kind: technique, surfaces: [gel, gels, electrophoresis,
     sdspage, "sds-page", page_gel, agarose_gel, nativegel, "2d-gel"]}

Section page ›

Dictionary word

Escherichia coli

escherichia_coli · Biochemistry pack

Kind: subject
Spelled: escherichia coli, e coli

As YAML for a pack file

  - {term: escherichia_coli, canonical: "Escherichia coli", theme_kind: subject,
     surfaces: ["escherichia coli", "e coli"]}

Section page ›

Dictionary word

extraction

extraction · Biochemistry pack

Kind: technique
Spelled: miniprep, midiprep, maxiprep, extraction, purification, purified, cleanup, phenol_chloroform and 1 more

As YAML for a pack file

  - {term: extraction, theme_kind: technique, surfaces: [miniprep, midiprep, maxiprep,
     extraction, purification, purified, cleanup, phenol_chloroform, columnprep]}

Section page ›

Dictionary word

flow cytometry

flow_cytometry · Biochemistry pack

Kind: technique
Spelled: facs, flow, cytometry, sorting, gating_strategy, compensation

As YAML for a pack file

  - {term: flow_cytometry, theme_kind: technique, surfaces: [facs, flow, cytometry, sorting,
     gating_strategy, compensation]}

Section page ›

Dictionary word

flow cytometry data

flow_cytometry_format · Biochemistry pack

Kind: format
Spelled: fcs

As YAML for a pack file

  - {term: flow_cytometry_format, canonical: "flow cytometry data", theme_kind: format,
     surfaces: [fcs], extension_only: [fcs]}

Section page ›

Dictionary word

FlowJo workspace

flowjo_workspace · Biochemistry pack

Kind: format
Spelled: wsp

As YAML for a pack file

  - {term: flowjo_workspace, canonical: "FlowJo workspace", theme_kind: format, surfaces: [wsp]}

Section page ›

Dictionary word

Gallus gallus

gallus_gallus · Biochemistry pack

Kind: subject
Spelled: gallus gallus, g gallus, chicken

As YAML for a pack file

  - {term: gallus_gallus, canonical: "Gallus gallus", theme_kind: subject,
     surfaces: ["gallus gallus", "g gallus", chicken]}

Section page ›

Dictionary word

genome editing

genome_editing · Biochemistry pack

Kind: technique
Spelled: crispr, cas9, cas12, base_editing, prime_editing, sgrna, grna, guide-rna and 2 more

As YAML for a pack file

  - {term: genome_editing, theme_kind: technique, surfaces: [crispr, cas9, cas12, base_editing,
     prime_editing, sgrna, grna, "guide-rna", talen, zfn]}

Section page ›

Dictionary word

genotype generic

genotype_generic · Biochemistry pack

Kind: subject
Spelled: mutant, mut, variant_strain, heterozygous, het, homozygous, hom, transgenic and 1 more

As YAML for a pack file

  - {term: genotype_generic, theme_kind: subject, surfaces: [mutant, mut, variant_strain,
     heterozygous, het, homozygous, hom, transgenic, parental]}

Section page ›

Dictionary word

glutathione S-transferase

glutathione_s_transferase · Biochemistry pack

Kind: reagent
Spelled: gst, glutathione s transferase

As YAML for a pack file

  - {term: glutathione_s_transferase, canonical: "glutathione S-transferase",
     theme_kind: reagent, surfaces: [gst, "glutathione s transferase"],
     ontology_ids: ["UniProt:P08515"]}

Section page ›

Dictionary word

GraphPad Prism project

prism_project · Biochemistry pack

Kind: format
Spelled: pzfx, prism

As YAML for a pack file

  - {term: prism_project, canonical: "GraphPad Prism project", theme_kind: format,
     surfaces: [pzfx, prism], extension_only: [prism], product: true}

Section page ›

Dictionary word

HEK293

hek293 · Biochemistry pack

Kind: subject
Spelled: hek 293, hek 293t

As YAML for a pack file

  - {term: hek293, canonical: HEK293, theme_kind: subject, surfaces: ["hek 293", "hek 293t"],
     ontology_ids: ["Cellosaurus:CVCL_0045", "Cellosaurus:CVCL_0063"]}

Section page ›

Dictionary word

HeLa

hela · Biochemistry pack

Kind: subject
Spelled: hela

As YAML for a pack file

  - {term: hela, canonical: HeLa, theme_kind: subject, surfaces: [hela],
     ontology_ids: ["Cellosaurus:CVCL_0030"]}

Section page ›

Dictionary word

Helicobacter pylori

helicobacter_pylori · Biochemistry pack

Kind: subject
Spelled: helicobacter pylori, h pylori, pylori

As YAML for a pack file

  - {term: helicobacter_pylori, canonical: "Helicobacter pylori", theme_kind: subject,
     surfaces: ["helicobacter pylori", "h pylori", pylori]}

Section page ›

Dictionary word

His tag

his_tag · Biochemistry pack

Kind: reagent
Spelled: his6, 6x his, 6 his, his tag, polyhistidine tag, histag

As YAML for a pack file

  - {term: his_tag, canonical: "His tag", theme_kind: reagent, surfaces: [his6, "6x his",
     "6 his", "his tag", "polyhistidine tag", histag]}

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Dictionary word

histamine

histamine · Biochemistry pack

Kind: reagent
Spelled: histamine

As YAML for a pack file

  - {term: histamine, theme_kind: reagent, surfaces: [histamine], ontology_ids: ["ChEBI:18295",
     "PubChem:774"]}

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Dictionary word

Homo sapiens

homo_sapiens · Biochemistry pack

Kind: subject
Spelled: homo sapiens, h sapiens

As YAML for a pack file

  - {term: homo_sapiens, canonical: "Homo sapiens", theme_kind: subject,
     surfaces: ["homo sapiens", "h sapiens"]}

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Dictionary word

Image Lab multichannel scan

imagelab_scan · Biochemistry pack

Kind: format
Spelled: mscn

As YAML for a pack file

  - {term: imagelab_scan, canonical: "Image Lab multichannel scan", theme_kind: format,
     surfaces: [mscn]}

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Dictionary word

immunoassay

immunoassay · Biochemistry pack

Kind: technique
Spelled: elisa, aliquot_elisa, sandwich_elisa, luminex, msd_assay, alphalisa

As YAML for a pack file

  - {term: immunoassay, theme_kind: technique, surfaces: [elisa, aliquot_elisa, sandwich_elisa,
     luminex, msd_assay, alphalisa]}

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Dictionary word

immunoblot

immunoblot · Biochemistry pack

Kind: technique
Spelled: western, western-blot, immunoblot, blot, wb

As YAML for a pack file

  - {term: immunoblot, theme_kind: technique, surfaces: [western, "western-blot", immunoblot,
     blot, wb]}

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Dictionary word

induction

induction · Biochemistry pack

Kind: reagent
Spelled: induced, induction, doxycycline, dox, iptg, tamoxifen, rapamycin, arabinose and 2 more

As YAML for a pack file

  - {term: induction, theme_kind: reagent, surfaces: [induced, induction, doxycycline, dox, iptg,
     tamoxifen, rapamycin, arabinose, tet_on, tet_off]}

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Dictionary word

inhibitor

inhibitor · Biochemistry pack

Kind: reagent
Spelled: inhibitor, inh, antagonist, blocker

As YAML for a pack file

  - {term: inhibitor, theme_kind: reagent, surfaces: [inhibitor, inh, antagonist, blocker]}

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Dictionary word

insulin

insulin · Biochemistry pack

Kind: reagent
Spelled: insulin

As YAML for a pack file

  - {term: insulin, theme_kind: reagent, surfaces: [insulin], ontology_ids: ["UniProt:P01308"]}

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Dictionary word

ionomycin

ionomycin · Biochemistry pack

Kind: reagent
Spelled: ionomycin

As YAML for a pack file

  - {term: ionomycin, theme_kind: reagent, surfaces: [ionomycin], ontology_ids: ["ChEBI:63954",
     "PubChem:6912226"]}

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Dictionary word

KDEL

kdel · Biochemistry pack

Kind: reagent
Spelled: kdel, er retention signal

As YAML for a pack file

  - {term: kdel, canonical: KDEL, theme_kind: reagent, surfaces: [kdel, "er retention signal"]}

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Dictionary word

knockdown

knockdown · Biochemistry pack

Kind: technique
Spelled: kd, knockdown, knock-down, sirna, shrna, rnai, morpholino, degron and 1 more

As YAML for a pack file

  - {term: knockdown, theme_kind: technique, surfaces: [kd, knockdown, "knock-down", sirna,
     shrna, rnai, morpholino, degron, auxin_degron]}

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Dictionary word

knockin

knockin · Biochemistry pack

Kind: technique
Spelled: ki, knockin, knock-in, tagged, endogenous_tag, homologous_recombination

As YAML for a pack file

  - {term: knockin, theme_kind: technique, surfaces: [ki, knockin, "knock-in", tagged,
     endogenous_tag, homologous_recombination]}

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Dictionary word

knockout

knockout · Biochemistry pack

Kind: technique
Spelled: ko, knockout, knock-out, null_allele, deletion_strain

As YAML for a pack file

  - {term: knockout, theme_kind: technique, surfaces: [ko, knockout, "knock-out", null_allele,
     deletion_strain]}

Section page ›

Dictionary word

mass photometry data

mass_photometry_data · Biochemistry pack

Kind: format
Spelled: mpr, mp, dmp

As YAML for a pack file

  - {term: mass_photometry_data, canonical: "mass photometry data", theme_kind: format,
     surfaces: [mpr, mp, dmp], extension_only: [mp]}

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Dictionary word

medium

medium · Biochemistry pack

Kind: reagent
Spelled: media, medium, dmem, rpmi, mem, emem, dmemf12, optimem and 5 more

As YAML for a pack file

  - {term: medium, theme_kind: reagent, surfaces: [media, medium, dmem, rpmi, mem, emem, dmemf12,
     optimem, "opti-mem", neurobasal, ymd, lb_broth, sc_media]}

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Dictionary word

microscopy prep

microscopy_prep · Biochemistry pack

Kind: technique
Spelled: fixation, fixed, pfa, formaldehyde, methanol_fix, permeabilisation, permeabilization, perm and 5 more

As YAML for a pack file

  - {term: microscopy_prep, theme_kind: technique, surfaces: [fixation, fixed, pfa, formaldehyde,
     methanol_fix, permeabilisation, permeabilization, perm, blocking, blocked, mounting, mountant,
     antifade]}

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Dictionary word

model organism generic

model_organism_generic · Biochemistry pack

Kind: subject
Spelled: invitro, in-vitro, invivo, in-vivo, insilico, in-silico

As YAML for a pack file

  - {term: model_organism_generic, theme_kind: subject, surfaces: [invitro, "in-vitro", invivo,
     "in-vivo", insilico, "in-silico"]}

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Dictionary word

molecular structure

structure_format · Biochemistry pack

Kind: format
Spelled: pdb, cif, mmcif, ent

As YAML for a pack file

  - {term: structure_format, canonical: "molecular structure", theme_kind: format,
     surfaces: [pdb, cif, mmcif, ent], extension_only: [cif]}

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Dictionary word

Mus musculus

mus_musculus · Biochemistry pack

Kind: subject
Spelled: mus musculus, m musculus, mouse, mice, murine

As YAML for a pack file

  - {term: mus_musculus, canonical: "Mus musculus", theme_kind: subject,
     surfaces: ["mus musculus", "m musculus", mouse, mice, murine]}

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Dictionary word

Myc tag

myc_tag · Biochemistry pack

Kind: reagent
Spelled: myc tag

As YAML for a pack file

  - {term: myc_tag, canonical: "Myc tag", theme_kind: reagent, surfaces: ["myc tag"]}

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Dictionary word

Mycobacterium tuberculosis

mycobacterium_tuberculosis · Biochemistry pack

Kind: subject
Spelled: mycobacterium tuberculosis, m tuberculosis

As YAML for a pack file

  - {term: mycobacterium_tuberculosis, canonical: "Mycobacterium tuberculosis",
     theme_kind: subject, surfaces: ["mycobacterium tuberculosis", "m tuberculosis"]}

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Dictionary word

Neurospora crassa

neurospora_crassa · Biochemistry pack

Kind: subject
Spelled: neurospora crassa, n crassa, neurospora

As YAML for a pack file

  - {term: neurospora_crassa, canonical: "Neurospora crassa", theme_kind: subject,
     surfaces: ["neurospora crassa", "n crassa", neurospora]}

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Dictionary word

Nicotiana benthamiana

nicotiana_benthamiana · Biochemistry pack

Kind: subject
Spelled: nicotiana benthamiana, n benthamiana, benthamiana

As YAML for a pack file

  - {term: nicotiana_benthamiana, canonical: "Nicotiana benthamiana", theme_kind: subject,
     surfaces: ["nicotiana benthamiana", "n benthamiana", benthamiana]}

Section page ›

Dictionary word

nocodazole

nocodazole · Biochemistry pack

Kind: reagent
Spelled: nocodazole

As YAML for a pack file

  - {term: nocodazole, theme_kind: reagent, surfaces: [nocodazole], ontology_ids: ["ChEBI:34892",
     "PubChem:4122"]}

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Dictionary word

novobiocin

novobiocin · Biochemistry pack

Kind: reagent
Spelled: novobiocin

As YAML for a pack file

  - {term: novobiocin, theme_kind: reagent, surfaces: [novobiocin], ontology_ids: ["ChEBI:28368",
     "PubChem:54675769"]}

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Dictionary word

nucleic blot

nucleic_blot · Biochemistry pack

Kind: technique
Spelled: southern, northern, dotblot, slotblot

As YAML for a pack file

  - {term: nucleic_blot, theme_kind: technique, surfaces: [southern, northern, dotblot,
     slotblot]}

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Dictionary word

oligomycin

oligomycin · Biochemistry pack

Kind: reagent
Spelled: oligomycin

As YAML for a pack file

  - {term: oligomycin, theme_kind: reagent, surfaces: [oligomycin],
     ontology_ids: ["ChEBI:25675"]}

Section page ›

Dictionary word

oligonucleotide

oligonucleotide · Biochemistry pack

Kind: reagent
Spelled: primer, primers, oligo, oligos, probe, probes, adapter_oligo

As YAML for a pack file

  - {term: oligonucleotide, theme_kind: reagent, surfaces: [primer, primers, oligo, oligos,
     probe, probes, adapter_oligo]}

Section page ›

Dictionary word

Oryzias latipes

oryzias_latipes · Biochemistry pack

Kind: subject
Spelled: oryzias latipes, o latipes, latipes, medaka

As YAML for a pack file

  - {term: oryzias_latipes, canonical: "Oryzias latipes", theme_kind: subject,
     surfaces: ["oryzias latipes", "o latipes", latipes, medaka]}

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Dictionary word

overexpression

overexpression · Biochemistry pack

Kind: technique
Spelled: oe, overexpression, over-expression, ectopic, induced_expression

As YAML for a pack file

  - {term: overexpression, theme_kind: technique, surfaces: [oe, overexpression,
     "over-expression", ectopic, induced_expression]}

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Dictionary word

passage

passage · Biochemistry pack

Kind: culture
Spelled: passage, p1, p2, p3, p4, p5, split_ratio, subculture

As YAML for a pack file

  - {term: passage, theme_kind: culture, surfaces: [passage, p1, p2, p3, p4, p5, split_ratio,
     subculture]}

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Dictionary word

phase separation

phase_separation · Biochemistry pack

Kind: subject
Spelled: phase separation, liquid-liquid phase separation, llps

As YAML for a pack file

  - {term: phase_separation, canonical: "phase separation", theme_kind: subject,
     surfaces: ["phase separation", "liquid-liquid phase separation", llps]}

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Dictionary word

plasma membrane

plasma_membrane · Biochemistry pack

Kind: subject
Spelled: plasma membrane

As YAML for a pack file

  - {term: plasma_membrane, canonical: "plasma membrane", theme_kind: subject,
     surfaces: ["plasma membrane"]}

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Dictionary word

Plasmodium falciparum

plasmodium_falciparum · Biochemistry pack

Kind: subject
Spelled: plasmodium falciparum, p falciparum, falciparum

As YAML for a pack file

  - {term: plasmodium_falciparum, canonical: "Plasmodium falciparum", theme_kind: subject,
     surfaces: ["plasmodium falciparum", "p falciparum", falciparum]}

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Dictionary word

plate imager experiment

plate_imager_experiment · Biochemistry pack

Kind: format
Spelled: xpt

As YAML for a pack file

  - {term: plate_imager_experiment, canonical: "plate imager experiment", theme_kind: format,
     surfaces: [xpt]}

Section page ›

Dictionary word

plate reader data

plate_reader_data · Biochemistry pack

Kind: format
Spelled: pda

As YAML for a pack file

  - {term: plate_reader_data, canonical: "plate reader data", theme_kind: format,
     surfaces: [pda]}

Section page ›

Dictionary word

polyethylene glycol

polyethylene_glycol · Biochemistry pack

Kind: reagent
Spelled: peg, peg4k, peg6k, peg8k, peg10k, peg20k, peg3350, peg4000 and 5 more

As YAML for a pack file

  - {term: polyethylene_glycol, canonical: "polyethylene glycol", theme_kind: reagent,
     surfaces: [peg, peg4k, peg6k, peg8k, peg10k, peg20k, peg3350, peg4000, peg6000, peg8000,
     peg10000, peg20000, "polyethylene glycol"], ontology_ids: ["ChEBI:46793"]}

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Dictionary word

polymerase chain reaction

polymerase_chain_reaction · Biochemistry pack

Kind: technique
Spelled: pcr, rtpcr, rt-pcr, qpcr, q-pcr, rtqpcr, ddpcr, digitalpcr and 2 more

As YAML for a pack file

  - {term: polymerase_chain_reaction, theme_kind: technique, surfaces: [pcr, rtpcr, "rt-pcr",
     qpcr, "q-pcr", rtqpcr, ddpcr, digitalpcr, nested_pcr, colony_pcr]}

Section page ›

Dictionary word

potassium chloride

potassium_chloride · Biochemistry pack

Kind: reagent
Spelled: kcl, potassium chloride

As YAML for a pack file

  - {term: potassium_chloride, canonical: "potassium chloride", theme_kind: reagent,
     surfaces: [kcl, "potassium chloride"], ontology_ids: ["ChEBI:32588", "PubChem:4873"]}

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Dictionary word

primary culture

primary_culture · Biochemistry pack

Kind: subject
Spelled: primary, primaries, ipsc, esc, organoid, spheroid, explant, ex_vivo

As YAML for a pack file

  - {term: primary_culture, theme_kind: subject, surfaces: [primary, primaries, ipsc, esc,
     organoid, spheroid, explant, ex_vivo]}

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Dictionary word

proteinase K

proteinase_k · Biochemistry pack

Kind: reagent
Spelled: proteinase k, protk

As YAML for a pack file

  - {term: proteinase_k, canonical: "proteinase K", theme_kind: reagent,
     surfaces: ["proteinase k", protk], ontology_ids: ["UniProt:P06873"]}

Section page ›

Dictionary word

PyMOL session

pymol_session · Biochemistry pack

Kind: format
Spelled: pse

As YAML for a pack file

  - {term: pymol_session, canonical: "PyMOL session", theme_kind: format, surfaces: [pse]}

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Dictionary word

quantitation

quantitation · Biochemistry pack

Kind: technique
Spelled: nanodrop, qubit, bioanalyzer, tapestation, a260, a280, 260/280, 260/230

As YAML for a pack file

  - {term: quantitation, theme_kind: technique, surfaces: [nanodrop, qubit, bioanalyzer,
     tapestation, a260, a280, "260/280", "260/230"]}

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Dictionary word

Rattus norvegicus

rattus_norvegicus · Biochemistry pack

Kind: subject
Spelled: rattus norvegicus, r norvegicus, norvegicus, rat

As YAML for a pack file

  - {term: rattus_norvegicus, canonical: "Rattus norvegicus", theme_kind: subject,
     surfaces: ["rattus norvegicus", "r norvegicus", norvegicus, rat]}

Section page ›

Dictionary word

restriction

restriction · Biochemistry pack

Kind: technique
Spelled: digest, digestion, restriction, linearised, linearized, enzyme_cut

As YAML for a pack file

  - {term: restriction, theme_kind: technique, surfaces: [digest, digestion, restriction,
     linearised, linearized, enzyme_cut]}

Section page ›

Dictionary word

Saccharomyces cerevisiae

saccharomyces_cerevisiae · Biochemistry pack

Kind: subject
Spelled: saccharomyces cerevisiae, s cerevisiae, cerevisiae, budding yeast

As YAML for a pack file

  - {term: saccharomyces_cerevisiae, canonical: "Saccharomyces cerevisiae", theme_kind: subject,
     surfaces: ["saccharomyces cerevisiae", "s cerevisiae", cerevisiae, "budding yeast"]}

Section page ›

Dictionary word

saponin

saponin · Biochemistry pack

Kind: reagent
Spelled: saponin

As YAML for a pack file

  - {term: saponin, theme_kind: reagent, surfaces: [saponin], ontology_ids: ["ChEBI:26605"]}

Section page ›

Dictionary word

Schizosaccharomyces pombe

schizosaccharomyces_pombe · Biochemistry pack

Kind: subject
Spelled: schizosaccharomyces pombe, s pombe, pombe, fission yeast

As YAML for a pack file

  - {term: schizosaccharomyces_pombe, canonical: "Schizosaccharomyces pombe",
     theme_kind: subject, surfaces: ["schizosaccharomyces pombe", "s pombe", pombe, "fission yeast"]}

Section page ›

Dictionary word

Schmidtea mediterranea

schmidtea_mediterranea · Biochemistry pack

Kind: subject
Spelled: schmidtea mediterranea, s mediterranea, schmidtea

As YAML for a pack file

  - {term: schmidtea_mediterranea, canonical: "Schmidtea mediterranea", theme_kind: subject,
     surfaces: ["schmidtea mediterranea", "s mediterranea", schmidtea]}

Section page ›

Dictionary word

selection

selection · Biochemistry pack

Kind: reagent
Spelled: selection, puromycin, blasticidin, hygromycin, neomycin, g418, zeocin, ampicillin and 2 more

As YAML for a pack file

  - {term: selection, theme_kind: reagent, surfaces: [selection, puromycin, blasticidin,
     hygromycin, neomycin, g418, zeocin, ampicillin, kanamycin, resistance_marker]}

Section page ›

Dictionary word

SnapGene plasmid

snapgene_plasmid · Biochemistry pack

Kind: format
Spelled: dna, prot, clxn

As YAML for a pack file

  - {term: snapgene_plasmid, canonical: "SnapGene plasmid", theme_kind: format, surfaces: [dna,
     prot, clxn], extension_only: [dna, prot]}

Section page ›

Dictionary word

sodium dodecyl sulfate

sodium_dodecyl_sulfate · Biochemistry pack

Kind: reagent
Spelled: sds, sodium dodecyl sulfate, sodium dodecyl sulphate

As YAML for a pack file

  - {term: sodium_dodecyl_sulfate, canonical: "sodium dodecyl sulfate", theme_kind: reagent,
     surfaces: [sds, "sodium dodecyl sulfate", "sodium dodecyl sulphate"],
     ontology_ids: ["ChEBI:8984"]}

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Dictionary word

Staphylococcus aureus

staphylococcus_aureus · Biochemistry pack

Kind: subject
Spelled: staphylococcus aureus, s aureus, aureus

As YAML for a pack file

  - {term: staphylococcus_aureus, canonical: "Staphylococcus aureus", theme_kind: subject,
     surfaces: ["staphylococcus aureus", "s aureus", aureus]}

Section page ›

Dictionary word

stress

stress · Biochemistry pack

Kind: condition
Spelled: heatshock, heat-shock, coldshock, oxidative, osmotic, starvation, hypoxia, nutrient_withdrawal

As YAML for a pack file

  - {term: stress, theme_kind: condition, surfaces: [heatshock, "heat-shock", coldshock,
     oxidative, osmotic, starvation, hypoxia, nutrient_withdrawal]}

Section page ›

Dictionary word

supplement

supplement · Biochemistry pack

Kind: reagent
Spelled: fbs, fcs, serum, penstrep, pen-strep, glutamine, glutamax, nea and 3 more

As YAML for a pack file

  - {term: supplement, theme_kind: reagent, surfaces: [fbs, fcs, serum, penstrep, "pen-strep",
     glutamine, glutamax, nea, b27, n2, hepes_supp]}

Section page ›

Dictionary word

Tetrahymena thermophila

tetrahymena_thermophila · Biochemistry pack

Kind: subject
Spelled: tetrahymena thermophila, t thermophila, tetrahymena, thermophila

As YAML for a pack file

  - {term: tetrahymena_thermophila, canonical: "Tetrahymena thermophila", theme_kind: subject,
     surfaces: ["tetrahymena thermophila", "t thermophila", tetrahymena, thermophila]}

Section page ›

Dictionary word

thapsigargin

thapsigargin · Biochemistry pack

Kind: reagent
Spelled: thapsigargin

As YAML for a pack file

  - {term: thapsigargin, theme_kind: reagent, surfaces: [thapsigargin],
     ontology_ids: ["ChEBI:9516", "PubChem:446378"]}

Section page ›

Dictionary word

Toxoplasma gondii

toxoplasma_gondii · Biochemistry pack

Kind: subject
Spelled: toxoplasma gondii, t gondii, toxoplasma, gondii

As YAML for a pack file

  - {term: toxoplasma_gondii, canonical: "Toxoplasma gondii", theme_kind: subject,
     surfaces: ["toxoplasma gondii", "t gondii", toxoplasma, gondii]}

Section page ›

Dictionary word

Triticum aestivum

triticum_aestivum · Biochemistry pack

Kind: subject
Spelled: triticum aestivum, t aestivum, aestivum, wheat

As YAML for a pack file

  - {term: triticum_aestivum, canonical: "Triticum aestivum", theme_kind: subject,
     surfaces: ["triticum aestivum", "t aestivum", aestivum, wheat]}

Section page ›

Dictionary word

Trypanosoma brucei

trypanosoma_brucei · Biochemistry pack

Kind: subject
Spelled: trypanosoma brucei, t brucei, brucei

As YAML for a pack file

  - {term: trypanosoma_brucei, canonical: "Trypanosoma brucei", theme_kind: subject,
     surfaces: ["trypanosoma brucei", "t brucei", brucei]}

Section page ›

Dictionary word

tunicamycin

tunicamycin · Biochemistry pack

Kind: reagent
Spelled: tunicamycin

As YAML for a pack file

  - {term: tunicamycin, theme_kind: reagent, surfaces: [tunicamycin],
     ontology_ids: ["ChEBI:29699"]}

Section page ›

Dictionary word

Tween 20

polysorbate_20 · Biochemistry pack

Kind: reagent
Spelled: tween 20, polysorbate 20

As YAML for a pack file

  - {term: polysorbate_20, canonical: "Tween 20", theme_kind: reagent, surfaces: ["tween 20",
     "polysorbate 20"], ontology_ids: ["ChEBI:53424"]}

Section page ›

Dictionary word

U2OS

u2os · Biochemistry pack

Kind: subject
Spelled: u2os, u 2 os, u20s

As YAML for a pack file

  - {term: u2os, canonical: U2OS, theme_kind: subject, surfaces: [u2os, "u 2 os", u20s],
     ontology_ids: ["Cellosaurus:CVCL_0042"]}

Section page ›

Dictionary word

UbC promoter

ubc_promoter · Biochemistry pack

Kind: reagent
Spelled: ubc promoter, ubiquitin c promoter

As YAML for a pack file

  - {term: ubc_promoter, canonical: "UbC promoter", theme_kind: reagent,
     surfaces: ["ubc promoter", "ubiquitin c promoter"]}

Section page ›

Dictionary word

vector

vector · Biochemistry pack

Kind: reagent
Spelled: plasmid, vector, backbone, insert, construct, cassette, promoter, terminator and 3 more

As YAML for a pack file

  - {term: vector, theme_kind: reagent, surfaces: [plasmid, vector, backbone, insert, construct,
     cassette, promoter, terminator, orf, cds, tag_sequence]}

Section page ›

Dictionary word

viral vector

viral_vector · Biochemistry pack

Kind: reagent
Spelled: lentivirus, lenti, retrovirus, aav, adenovirus, baculovirus, vsvg

As YAML for a pack file

  - {term: viral_vector, theme_kind: reagent, surfaces: [lentivirus, lenti, retrovirus, aav,
     adenovirus, baculovirus, vsvg]}

Section page ›

Dictionary word

washout

washout · Biochemistry pack

Kind: condition
Spelled: washout, wash-out, recovery_period, chase, pulse_chase

As YAML for a pack file

  - {term: washout, theme_kind: condition, surfaces: [washout, "wash-out", recovery_period,
     chase, pulse_chase]}

Section page ›

Dictionary word

Xenopus laevis

xenopus_laevis · Biochemistry pack

Kind: subject
Spelled: xenopus laevis, x laevis, laevis, african clawed frog

As YAML for a pack file

  - {term: xenopus_laevis, canonical: "Xenopus laevis", theme_kind: subject,
     surfaces: ["xenopus laevis", "x laevis", laevis, "african clawed frog"]}

Section page ›

Dictionary word

Xenopus tropicalis

xenopus_tropicalis · Biochemistry pack

Kind: subject
Spelled: xenopus tropicalis, x tropicalis, tropicalis, western clawed frog

As YAML for a pack file

  - {term: xenopus_tropicalis, canonical: "Xenopus tropicalis", theme_kind: subject,
     surfaces: ["xenopus tropicalis", "x tropicalis", tropicalis, "western clawed frog"]}

Section page ›

Dictionary word

Zea mays

zea_mays · Biochemistry pack

Kind: subject
Spelled: zea mays, z mays, maize

As YAML for a pack file

  - {term: zea_mays, canonical: "Zea mays", theme_kind: subject, surfaces: ["zea mays", "z mays",
     maize]}

Section page ›

Clinical pack 18 words

Study design, specimens, imaging modalities, and identifier vocabulary. Version 2. A project loads a pack by name. Pack page

Word	Kind	Means	Pack
blood product	sample	Spelled `serum`, `plasma`, `wholeblood`, `whole-blood`, `buffycoat` and 2 more	Clinical pack
clinical imaging	technique	Spelled `ct`, `mri`, `fmri`, `pet`, `spect` and 9 more	Clinical pack
deidentified	quality	Spelled `deidentified`, `de-identified`, `anonymised`, `anonymized`, `pseudonymised` and 4 more	Clinical pack
direct identifier	identifier	Spelled `name_field`, `surname`, `forename`, `dob`, `dateofbirth` and 6 more	Clinical pack
fluid specimen	sample	Spelled `urine`, `csf`, `saliva`, `sputum`, `bal` and 5 more	Clinical pack
governance	file role	Spelled `consent`, `icf`, `irb`, `ethics`, `protocol_approval` and 3 more	Clinical pack
histology	technique	Spelled `he_stain`, `h&e`, `ihc_clinical`, `ish`, `fish` and 4 more	Clinical pack
imaging format	format	Spelled `dicom`, `dcm`, `nifti`, `nii`, `analyze_format` and 2 more	Clinical pack
imaging sequence	technique	Spelled `t1`, `t2`, `flair`, `dwi`, `adc_map` and 4 more	Clinical pack
outcome	statistic	Spelled `endpoint`, `primaryendpoint`, `secondaryendpoint`, `outcome`, `response` and 4 more	Clinical pack
participant identifier	identifier	Spelled `subjectid`, `subject-id`, `patientid`, `participantid`, `studyid` and 2 more	Clinical pack
randomisation	technique	Spelled `randomised`, `randomized`, `rct`, `blinded`, `doubleblind` and 4 more	Clinical pack
record identifier	identifier	Spelled `mrn`, `medical-record-number`, `nhsnumber`, `ssn`, `insuranceid` and 2 more	Clinical pack
safety	statistic	Spelled `adverse`, `ae_event`, `sae`, `toxicity`, `grade_tox` and 2 more	Clinical pack
study arm	condition	Spelled `placebo`, `comparator`, `activearm`, `standardofcare`, `soc` and 1 more	Clinical pack
tissue specimen	sample	Spelled `biopsy`, `resection`, `ffpe`, `frozensection`, `fresh-frozen` and 3 more	Clinical pack
trial phase	technique	Spelled `phase1`, `phase2`, `phase3`, `phase4`, `phase-i` and 4 more	Clinical pack
visit	timepoint	Spelled `visit`, `screening`, `enrollment`, `enrolment`, `baseline_visit` and 5 more	Clinical pack

Dictionary word

blood product

blood_product · Clinical pack

Kind: sample
Spelled: serum, plasma, wholeblood, whole-blood, buffycoat, pbmc, dbs

As YAML for a pack file

  - {term: blood_product, theme_kind: sample, surfaces: [serum, plasma, wholeblood,
     "whole-blood", buffycoat, pbmc, dbs]}

Section page ›

Dictionary word

clinical imaging

clinical_imaging · Clinical pack

Kind: technique
Spelled: ct, mri, fmri, pet, spect, ultrasound, us_imaging, xray and 6 more
Ambiguous: Yes. Also read as x ray tomography

As YAML for a pack file

  - {term: clinical_imaging, theme_kind: technique, surfaces: [ct, mri, fmri, pet, spect,
     ultrasound, us_imaging, xray, "x-ray", "x-ray ct", radiograph, mammogram, dexa, oct_imaging],
     ambiguous_with: [x_ray_tomography]}

Section page ›

Dictionary word

deidentified

deidentified · Clinical pack

Kind: quality
Spelled: deidentified, de-identified, anonymised, anonymized, pseudonymised, pseudonymized, coded, scrubbed and 1 more

As YAML for a pack file

  - {term: deidentified, theme_kind: quality, surfaces: [deidentified, "de-identified",
     anonymised, anonymized, pseudonymised, pseudonymized, coded, scrubbed, redacted]}

Section page ›

Dictionary word

direct identifier

direct_identifier · Clinical pack

Kind: identifier
Spelled: name_field, surname, forename, dob, dateofbirth, date-of-birth, address, postcode and 3 more

As YAML for a pack file

  - {term: direct_identifier, theme_kind: identifier, surfaces: [name_field, surname, forename,
     dob, dateofbirth, "date-of-birth", address, postcode, zipcode, phone, email_field],
     sensitive: true}

Section page ›

Dictionary word

fluid specimen

fluid_specimen · Clinical pack

Kind: sample
Spelled: urine, csf, saliva, sputum, bal, ascites, synovial, stool and 2 more

As YAML for a pack file

  - {term: fluid_specimen, theme_kind: sample, surfaces: [urine, csf, saliva, sputum, bal,
     ascites, synovial, stool, faecal, fecal]}

Section page ›

Dictionary word

governance

governance · Clinical pack

Kind: file role
Spelled: consent, icf, irb, ethics, protocol_approval, amendment, deviation, monitoring

As YAML for a pack file

  - {term: governance, theme_kind: file_role, surfaces: [consent, icf, irb, ethics,
     protocol_approval, amendment, deviation, monitoring]}

Section page ›

Dictionary word

histology

histology · Clinical pack

Kind: technique
Spelled: he_stain, h&e, ihc_clinical, ish, fish, trichrome, pas_stain, giemsa and 1 more

As YAML for a pack file

  - {term: histology, theme_kind: technique, surfaces: [he_stain, "h&e", ihc_clinical, ish, fish,
     trichrome, pas_stain, giemsa, papanicolaou]}

Section page ›

Dictionary word

imaging format

imaging_format · Clinical pack

Kind: format
Spelled: dicom, dcm, nifti, nii, analyze_format, minc, par_rec

As YAML for a pack file

  - {term: imaging_format, theme_kind: format, surfaces: [dicom, dcm, nifti, nii, analyze_format,
     minc, par_rec]}

Section page ›

Dictionary word

imaging sequence

imaging_sequence · Clinical pack

Kind: technique
Spelled: t1, t2, flair, dwi, adc_map, dti, bold, contrast_enhanced and 1 more

As YAML for a pack file

  - {term: imaging_sequence, theme_kind: technique, surfaces: [t1, t2, flair, dwi, adc_map, dti,
     bold, contrast_enhanced, gadolinium]}

Section page ›

Dictionary word

outcome

outcome · Clinical pack

Kind: statistic
Spelled: endpoint, primaryendpoint, secondaryendpoint, outcome, response, progression, survival, os_survival and 1 more

As YAML for a pack file

  - {term: outcome, theme_kind: statistic, surfaces: [endpoint, primaryendpoint,
     secondaryendpoint, outcome, response, progression, survival, os_survival, pfs]}

Section page ›

Dictionary word

participant identifier

participant_identifier · Clinical pack

Kind: identifier
Spelled: subjectid, subject-id, patientid, participantid, studyid, screeningnumber, randomisationnumber

As YAML for a pack file

  - {term: participant_identifier, theme_kind: identifier, surfaces: [subjectid, "subject-id",
     patientid, participantid, studyid, screeningnumber, randomisationnumber], sensitive: true}

Section page ›

Dictionary word

randomisation

randomisation · Clinical pack

Kind: technique
Spelled: randomised, randomized, rct, blinded, doubleblind, double-blind, openlabel, crossover and 1 more

As YAML for a pack file

  - {term: randomisation, theme_kind: technique, surfaces: [randomised, randomized, rct, blinded,
     doubleblind, "double-blind", openlabel, crossover, parallel_arm]}

Section page ›

Dictionary word

record identifier

record_identifier · Clinical pack

Kind: identifier
Spelled: mrn, medical-record-number, nhsnumber, ssn, insuranceid, accession, accessionnumber

As YAML for a pack file

  - {term: record_identifier, theme_kind: identifier, surfaces: [mrn, "medical-record-number",
     nhsnumber, ssn, insuranceid, accession, accessionnumber], sensitive: true}

Section page ›

Dictionary word

safety

safety · Clinical pack

Kind: statistic
Spelled: adverse, ae_event, sae, toxicity, grade_tox, dlt, safetyreport

As YAML for a pack file

  - {term: safety, theme_kind: statistic, surfaces: [adverse, ae_event, sae, toxicity, grade_tox,
     dlt, safetyreport]}

Section page ›

Dictionary word

study arm

study_arm · Clinical pack

Kind: condition
Spelled: placebo, comparator, activearm, standardofcare, soc, intervention

As YAML for a pack file

  - {term: study_arm, theme_kind: condition, surfaces: [placebo, comparator, activearm,
     standardofcare, soc, intervention]}

Section page ›

Dictionary word

tissue specimen

tissue_specimen · Clinical pack

Kind: sample
Spelled: biopsy, resection, ffpe, frozensection, fresh-frozen, oct_embedded, tma, autopsy

As YAML for a pack file

  - {term: tissue_specimen, theme_kind: sample, surfaces: [biopsy, resection, ffpe,
     frozensection, "fresh-frozen", oct_embedded, tma, autopsy]}

Section page ›

Dictionary word

trial phase

trial_phase · Clinical pack

Kind: technique
Spelled: phase1, phase2, phase3, phase4, phase-i, phase-ii, phase-iii, pilot and 1 more

As YAML for a pack file

  - {term: trial_phase, theme_kind: technique, surfaces: [phase1, phase2, phase3, phase4,
     "phase-i", "phase-ii", "phase-iii", pilot, feasibility]}

Section page ›

Dictionary word

visit

visit · Clinical pack

Kind: timepoint
Spelled: visit, screening, enrollment, enrolment, baseline_visit, followup, follow-up, endofstudy and 2 more

As YAML for a pack file

  - {term: visit, theme_kind: timepoint, surfaces: [visit, screening, enrollment, enrolment,
     baseline_visit, followup, "follow-up", endofstudy, eos, unscheduled]}

Section page ›

Computational pack 27 words

Simulation, numerical methods, scheduling and scientific file formats. Version 2. A project loads a pack by name. Pack page

Word	Kind	Means	Pack
agent based	technique	Spelled `abm`, `agentbased`, `agent-based`, `cellularautomaton`	Computational pack
array format	format	Spelled `npy`, `npz`, `hdf5`, `h5`, `nc` and 4 more	Computational pack
boundary condition	condition	Spelled `bc`, `boundarycondition`, `boundary-condition`, `periodic`, `dirichlet` and 1 more	Computational pack
checkpoint	file role	Spelled `checkpoint`, `ckpt`, `restart`, `resume_state`, `statefile`	Computational pack
compute resource	measurement	Spelled `node`, `nodes`, `core`, `cores`, `cpu` and 9 more	Computational pack
container runtime	software	Spelled `docker`, `singularity`, `apptainer`, `podman`, `conda_env` and 2 more	Computational pack
convergence	statistic	Spelled `converged`, `convergence`, `tolerance`, `residual_sim`, `iteration_count`	Computational pack
ensemble	condition	Spelled `nvt`, `npt`, `nve`, `ensemble`, `equilibration` and 2 more	Computational pack
finite element	technique	Spelled `fem`, `finiteelement`, `fenics`, `abaqus`, `comsol_run` and 1 more	Computational pack
image software	software	Spelled `imagej`, `fiji`, `ilastik_sw`, `cellprofiler`, `napari` and 10 more	Computational pack
initial condition	condition	Spelled `ic`, `initialcondition`, `initial-condition`, `seed_state`, `startingconfig`	Computational pack
language	software	Spelled `python`, `r_lang`, `matlab`, `julia`, `cpp` and 5 more	Computational pack
MATLAB figure `matlab_figure`	format	Spelled `fig`	Computational pack
mesh	measurement	Spelled `mesh`, `grid`, `lattice`, `discretisation`, `discretization` and 2 more	Computational pack
molecular dynamics	technique	Spelled `md`, `moleculardynamics`, `gromacs`, `amber`, `namd` and 3 more	Computational pack
monte carlo	technique	Spelled `mc`, `montecarlo`, `monte-carlo`, `metropolis`, `gibbs_sampling` and 1 more	Computational pack
parameter sweep	condition	Spelled `sweep`, `paramsweep`, `parameter-sweep`, `gridsearch`, `grid-search` and 1 more	Computational pack
quantum chemistry	technique	Spelled `dft`, `abinitio`, `ab-initio`, `hartreefock`, `hf_qc` and 5 more	Computational pack
RStudio project `rstudio_project`	format	Spelled `rproj`	Computational pack
scheduler	software	Spelled `slurm`, `sbatch`, `srun`, `pbs`, `torque` and 5 more	Computational pack
scientific library	software	Spelled `numpy`, `scipy`, `pandas`, `scikit`, `sklearn` and 8 more	Computational pack
simulation	technique	Spelled `sim`, `simulation`, `simulated`, `insilico_run`, `synthetic_data`	Computational pack
timestep	measurement	Spelled `dt`, `timestep`, `time-step`, `stepsize_sim`, `integrator`	Computational pack
trained classifier	format	Spelled `model`	Computational pack
trajectory	acquisition	Spelled `traj`, `trajectory`, `dump_file`, `frames_sim`, `snapshot_sim`	Computational pack
version control tool	software	Spelled `git`, `svn_tool`, `mercurial`, `commit_ref`, `branch_name` and 1 more	Computational pack
workflow manager	software	Spelled `snakemake`, `nextflow`, `cwl`, `wdl`, `luigi` and 4 more	Computational pack

Dictionary word

agent based

agent_based · Computational pack

Kind: technique
Spelled: abm, agentbased, agent-based, cellularautomaton

As YAML for a pack file

  - {term: agent_based, theme_kind: technique, surfaces: [abm, agentbased, "agent-based",
     cellularautomaton]}

Section page ›

Dictionary word

array format

array_format · Computational pack

Kind: format
Spelled: npy, npz, hdf5, h5, nc, netcdf, zarr, mat and 1 more

As YAML for a pack file

  - {term: array_format, theme_kind: format, surfaces: [npy, npz, hdf5, h5, nc, netcdf, zarr,
     mat, n5], extension_only: [mat, nc, netcdf, n5]}

Section page ›

Dictionary word

boundary condition

boundary_condition · Computational pack

Kind: condition
Spelled: bc, boundarycondition, boundary-condition, periodic, dirichlet, neumann

As YAML for a pack file

  - {term: boundary_condition, theme_kind: condition, surfaces: [bc, boundarycondition,
     "boundary-condition", periodic, dirichlet, neumann]}

Section page ›

Dictionary word

checkpoint

checkpoint · Computational pack

Kind: file role
Spelled: checkpoint, ckpt, restart, resume_state, statefile

As YAML for a pack file

  - {term: checkpoint, theme_kind: file_role, surfaces: [checkpoint, ckpt, restart, resume_state,
     statefile]}

Section page ›

Dictionary word

compute resource

compute_resource · Computational pack

Kind: measurement
Spelled: node, nodes, core, cores, cpu, gpu, mpi, rank and 6 more

As YAML for a pack file

  - {term: compute_resource, theme_kind: measurement, surfaces: [node, nodes, core, cores, cpu,
     gpu, mpi, rank, thread, threads, walltime, partition, queue_name, jobid]}

Section page ›

Dictionary word

container runtime

container_runtime · Computational pack

Kind: software
Spelled: docker, singularity, apptainer, podman, conda_env, venv, module_load

As YAML for a pack file

  - {term: container_runtime, theme_kind: software, surfaces: [docker, singularity, apptainer,
     podman, conda_env, venv, module_load]}

Section page ›

Dictionary word

convergence

convergence · Computational pack

Kind: statistic
Spelled: converged, convergence, tolerance, residual_sim, iteration_count

As YAML for a pack file

  - {term: convergence, theme_kind: statistic, surfaces: [converged, convergence, tolerance,
     residual_sim, iteration_count]}

Section page ›

Dictionary word

ensemble

ensemble · Computational pack

Kind: condition
Spelled: nvt, npt, nve, ensemble, equilibration, production_run, annealing

As YAML for a pack file

  - {term: ensemble, theme_kind: condition, surfaces: [nvt, npt, nve, ensemble, equilibration,
     production_run, annealing]}

Section page ›

Dictionary word

finite element

finite_element · Computational pack

Kind: technique
Spelled: fem, finiteelement, fenics, abaqus, comsol_run, mesh_solver

As YAML for a pack file

  - {term: finite_element, theme_kind: technique, surfaces: [fem, finiteelement, fenics, abaqus,
     comsol_run, mesh_solver]}

Section page ›

Dictionary word

image software

image_software · Computational pack

Kind: software
Spelled: imagej, fiji, ilastik_sw, cellprofiler, napari, icy, imaris, arivis and 7 more

As YAML for a pack file

  - {term: image_software, theme_kind: software, surfaces: [imagej, fiji, ilastik_sw,
     cellprofiler, napari, icy, imaris, arivis, omero, qupath, huygens, nis_elements, zen_sw,
     metamorph, micromanager]}

Section page ›

Dictionary word

initial condition

initial_condition · Computational pack

Kind: condition
Spelled: ic, initialcondition, initial-condition, seed_state, startingconfig

As YAML for a pack file

  - {term: initial_condition, theme_kind: condition, surfaces: [ic, initialcondition,
     "initial-condition", seed_state, startingconfig]}

Section page ›

Dictionary word

language

language · Computational pack

Kind: software
Spelled: python, r_lang, matlab, julia, cpp, fortran, java_lang, javascript and 2 more

As YAML for a pack file

  - {term: language, theme_kind: software, surfaces: [python, r_lang, matlab, julia, cpp,
     fortran, java_lang, javascript, shell_lang, perl]}

Section page ›

Dictionary word

MATLAB figure

matlab_figure · Computational pack

Kind: format
Spelled: fig

As YAML for a pack file

  - {term: matlab_figure, canonical: "MATLAB figure", theme_kind: format, surfaces: [fig],
     extension_only: [fig]}

Section page ›

Dictionary word

mesh

mesh · Computational pack

Kind: measurement
Spelled: mesh, grid, lattice, discretisation, discretization, nodes_mesh, elements_mesh

As YAML for a pack file

  - {term: mesh, theme_kind: measurement, surfaces: [mesh, grid, lattice, discretisation,
     discretization, nodes_mesh, elements_mesh]}

Section page ›

Dictionary word

molecular dynamics

molecular_dynamics · Computational pack

Kind: technique
Spelled: md, moleculardynamics, gromacs, amber, namd, lammps, openmm, charmm
Ambiguous: Yes. Also read as markdown

As YAML for a pack file

  - {term: molecular_dynamics, theme_kind: technique, surfaces: [md, moleculardynamics, gromacs,
     amber, namd, lammps, openmm, charmm], ambiguous_with: [markdown]}

Section page ›

Dictionary word

monte carlo

monte_carlo · Computational pack

Kind: technique
Spelled: mc, montecarlo, monte-carlo, metropolis, gibbs_sampling, mcmc

As YAML for a pack file

  - {term: monte_carlo, theme_kind: technique, surfaces: [mc, montecarlo, "monte-carlo",
     metropolis, gibbs_sampling, mcmc]}

Section page ›

Dictionary word

parameter sweep

parameter_sweep · Computational pack

Kind: condition
Spelled: sweep, paramsweep, parameter-sweep, gridsearch, grid-search, scan_params

As YAML for a pack file

  - {term: parameter_sweep, theme_kind: condition, surfaces: [sweep, paramsweep,
     "parameter-sweep", gridsearch, "grid-search", scan_params]}

Section page ›

Dictionary word

quantum chemistry

quantum_chemistry · Computational pack

Kind: technique
Spelled: dft, abinitio, ab-initio, hartreefock, hf_qc, gaussian_calc, orca, psi4 and 2 more

As YAML for a pack file

  - {term: quantum_chemistry, theme_kind: technique, surfaces: [dft, abinitio, "ab-initio",
     hartreefock, hf_qc, gaussian_calc, orca, psi4, vasp, quantumespresso]}

Section page ›

Dictionary word

RStudio project

rstudio_project · Computational pack

Kind: format
Spelled: rproj

As YAML for a pack file

  - {term: rstudio_project, canonical: "RStudio project", theme_kind: format, surfaces: [rproj]}

Section page ›

Dictionary word

scheduler

scheduler · Computational pack

Kind: software
Spelled: slurm, sbatch, srun, pbs, torque, sge, qsub, lsf and 2 more

As YAML for a pack file

  - {term: scheduler, theme_kind: software, surfaces: [slurm, sbatch, srun, pbs, torque, sge,
     qsub, lsf, bsub, condor]}

Section page ›

Dictionary word

scientific library

scientific_library · Computational pack

Kind: software
Spelled: numpy, scipy, pandas, scikit, sklearn, tensorflow, pytorch, jax and 5 more

As YAML for a pack file

  - {term: scientific_library, theme_kind: software, surfaces: [numpy, scipy, pandas, scikit,
     sklearn, tensorflow, pytorch, jax, tidyverse, ggplot, bioconductor, seurat, scanpy]}

Section page ›

Dictionary word

simulation

simulation · Computational pack

Kind: technique
Spelled: sim, simulation, simulated, insilico_run, synthetic_data
Ambiguous: Yes. Also read as structured illumination

As YAML for a pack file

  - {term: simulation, theme_kind: technique, surfaces: [sim, simulation, simulated,
     insilico_run, synthetic_data], ambiguous_with: [structured_illumination]}

Section page ›

Dictionary word

timestep

timestep · Computational pack

Kind: measurement
Spelled: dt, timestep, time-step, stepsize_sim, integrator

As YAML for a pack file

  - {term: timestep, theme_kind: measurement, surfaces: [dt, timestep, "time-step", stepsize_sim,
     integrator]}

Section page ›

Dictionary word

trained classifier

trained_classifier · Computational pack

Kind: format
Spelled: model

As YAML for a pack file

  - {term: trained_classifier, canonical: "trained classifier", theme_kind: format,
     surfaces: [model], extension_only: [model]}

Section page ›

Dictionary word

trajectory

trajectory · Computational pack

Kind: acquisition
Spelled: traj, trajectory, dump_file, frames_sim, snapshot_sim

As YAML for a pack file

  - {term: trajectory, theme_kind: acquisition, surfaces: [traj, trajectory, dump_file,
     frames_sim, snapshot_sim]}

Section page ›

Dictionary word

version control tool

version_control_tool · Computational pack

Kind: software
Spelled: git, svn_tool, mercurial, commit_ref, branch_name, tag_ref

As YAML for a pack file

  - {term: version_control_tool, theme_kind: software, surfaces: [git, svn_tool, mercurial,
     commit_ref, branch_name, tag_ref]}

Section page ›

Dictionary word

workflow manager

workflow_manager · Computational pack

Kind: software
Spelled: snakemake, nextflow, cwl, wdl, luigi, airflow, prefect, make and 1 more

As YAML for a pack file

  - {term: workflow_manager, theme_kind: software, surfaces: [snakemake, nextflow, cwl, wdl,
     luigi, airflow, prefect, make, cmake]}

Section page ›

Programs pack 1 words

Named scientific suites, recognised by the parts their installations hold side by side. Version 1. A project loads a pack by name. Pack page

Word	Kind	Means	Pack	Copy
TrackMate `trackmate`	software	Spelled `trackmate`	Programs pack

Dictionary word

TrackMate

trackmate · Programs pack

Kind: software
Spelled: trackmate

As YAML for a pack file

  - {term: trackmate, canonical: TrackMate, theme_kind: software, surfaces: [trackmate]}

Section page ›

Rulebook 114 rules

Every rule the engine ships, in the order it applies them. Ingence concludes nothing without one. All rules

Rule	Kind	Means	Pack	Copy
Cascade container member `cascade.container_member`	What the walk itself records	A ZIP or other container holds only what opening it found, and the Index notes whether opening finished, stopped at a limit or was refused; an archive link is read from its text and never opened.	Rulebook	provisional
Census directory aggregate `census.directory_aggregate`	What the walk itself records	A folder holds exactly the files, folders and bytes the walk counted inside it and beneath it.	Rulebook	provisional
Census filesystem containment `census.filesystem_containment`	What the walk itself records	A folder holds every file and folder the walk found directly inside it.	Rulebook	provisional
Census object kind `census.object_kind`	What the walk itself records	Anything on the disk that is not a file, a folder or a shortcut is recorded as what it is, such as a pipe or a device.	Rulebook	provisional
Acquisition stage from format `acquisition_stage_from_format`	What files are	A file in an image or electrophysiology format that an instrument writes is placed at the recording step, unless its contents contradict its extension or its own name says it was processed.	Rulebook
Analysis stage from derived sense `analysis_stage_from_derived_sense`	What files are	A file whose name says it holds a trajectory, which is worked out from recordings rather than recorded, is placed at the analysis step, unless it is a program.	Rulebook
Condition from quantities `condition_from_quantities`	What files are	A file whose name carries an amount, such as 10uM or 37C, is taken to record the condition it was made under.	Rulebook
Condition inherited from folder `condition_inherited_from_folder`	What files are	Not available in this version. A file whose name states no condition takes the condition its folder's name states.	Rulebook
Date neighbourhood of a file `date_neighbourhood_of_a_file`	What files are	A date in a file's name, or else in the nearest folder name above it, says roughly when it belongs, never exactly when it was made; two dates make a span.	Rulebook
Date neighbourhood of a folder `date_neighbourhood_of_a_folder`	What files are	A date in a folder's name says roughly when what it holds belongs; two dates make a span.	Rulebook
Declared digest contradicted `declared_digest_contradicted`	What files are	A file whose bytes the engine read under the same checksum method its archive used, and found a different checksum, does not hold what the archive said.	Rulebook
Declared sha256 contradicted `declared_sha256_contradicted`	What files are	A file whose bytes, read here, give another SHA-256 than its archive declared is marked so, and the reading here is the fact.	Rulebook
Earliest credible time `earliest_credible_time`	What files are	Each file is given the earliest time it is known to have existed: a time written inside it, where one was read, and otherwise the earlier of its creation and its last change, since a copy is created after it was last changed; an impossible time, such as one from 1969 or one later than the scan that saw the file, is set aside; a document's creation date that is really the date of the blank template it was made from (midnight, years before the document was saved) is kept but not believed; where the time came from is kept with it, and a stand-in file is left out.	Rulebook
Empty replicate is no data point `empty_replicate_is_no_data_point`	What files are	An empty file sitting among files of the same kind that hold data, such as one movie's empty tracking table beside the others' full ones, is taken as no data point and is left out when an analysis is weighed.	Rulebook
Experiment folder from contents `experiment_folder_from_contents`	What files are	A folder is taken as one experiment when it holds an instrument's raw files together with files named after them, such as drift-corrected copies and results tables, and no folder above it holds the same ones, or as one session's raw files when it holds only those, or as an analysis when it holds only files named after raw files kept elsewhere, or as an analysis when it holds one program's many folders side by side, one per movie or cell, each with the same few files, all without reading what any word means.	Rulebook
Experiment folder from dated name `experiment_folder_from_dated_name`	What files are	A folder whose name holds a date beside other words is taken as an experiment, unless a folder above it already has such a name, or it is one of many folders a program wrote, one per movie or cell.	Rulebook
File role unless program `file_role_unless_program`	What files are	A file is taken to serve the purpose its name states, such as a protocol or notes, unless it is a program or sits inside an installed program.	Rulebook
Filesystem noise from spelling `filesystem_noise_from_spelling`	What files are	Files a computer makes on its own, such as .DS_Store or Thumbs.db, are recognized by how their names are spelled and set aside; an office program's lock file, whose name starts ~$, is left alone, because it means somebody was at work.	Rulebook
Folder copied by declared clocks `folder_copied_by_declared_clocks`	What files are	A folder whose files an archive says it received together, on one day, was copied there whole on that day; the archive's time is the copy's, never when the files were made, so nothing is put in order by it.	Rulebook
Folder copied in bulk `folder_copied_in_bulk`	What files are	A folder whose files were all created within minutes of one another, after they were last changed, was copied here whole on that day, which explains its creation times and asks nothing.	Rulebook
Format from extension unless contradicted `format_from_extension_unless_contradicted`	What files are	A file is taken to be in the format its extension names, when that extension means one format and nothing else, unless its contents begin the way another format does; a container the format is built on, such as HDF5 or ZIP, does not count.	Rulebook
Later stage from name `later_stage_from_name`	What files are	A file's name says it is past the point of recording when it has a word such as processed, filtered, stitched or merged in it; instrument software saves such files in its own format too.	Rulebook
Miscellaneous files approved `miscellaneous_files_approved`	What files are	A folder someone kept as their miscellaneous files is claimed so, and nothing in it is moved into an experiment.	Rulebook
Naming is authored or emitted `naming_is_authored_or_emitted`	What files are	Not available in this version. A name is taken as typed by a person when it holds a word a machine would not write, and as written by a machine when three or more names beside it differ only by a counter.	Rulebook
Note written as a file name `note_written_as_a_file_name`	What files are	An empty text file whose name is a sentence is a note someone left, and its name is what it says, so it is never counted as an empty file.	Rulebook
Organising folder from name `organising_folder_from_name`	What files are	A folder named for analysis, summaries, exports, loose files or in-between steps is taken to organize work rather than to hold one piece of it.	Rulebook
Pipeline stage from name `pipeline_stage_from_name`	What files are	A file is placed at the step of the work its name states, such as raw, processed or analysis, unless it is a program or sits inside an installed program.	Rulebook
Placeholder from entry kind `placeholder_from_entry_kind`	What files are	A shortcut, or a file that claims a size but takes up no room on the disk, is taken to stand in for contents kept somewhere else.	Rulebook
Program from extension `program_from_extension`	What files are	Files whose extensions come from programming or macro languages, such as .py, .R or an ImageJ macro, are recognized as programs, unless their contents say otherwise.	Rulebook
Replicate from indexed label `replicate_from_indexed_label`	What files are	A file is taken to be the repeat its name numbers, such as rep2, unless it is a program.	Rulebook
Roi archive from members `roi_archive_from_members`	What files are	A ZIP is recognized as a Fiji set of regions of interest when a look inside found that every item is a .roi file beginning the way Fiji's regions do, unless the ZIP is a stand-in.	Rulebook
Series member from index `series_member_from_index`	What files are	A file whose name carries a numbered label, such as cell3, is taken to be one member of a series rather than a thing on its own.	Rulebook
Stage inherited from folder `stage_inherited_from_folder`	What files are	Not available in this version. A file whose name states no step of the work takes the step its folder's name states.	Rulebook
Technique from name `technique_from_name`	What files are	A file is taken to be about the techniques its name mentions, when its name mentions at least two.	Rulebook
Version from name `version_from_name`	What files are	A file whose name carries a version, such as v2, is taken to be one version of something rather than the whole of it.	Rulebook
Archive link copy of a file `archive_link_copy_of_a_file`	Which files go together	A link an archive left in place of a file is a copy of the file of its name held elsewhere in the folders read, matched by name and by the folders its text names; nothing is opened.	Rulebook
Copies a person answered `copies_a_person_answered`	Which files go together	A set of files someone called copies is grouped as copies, and a set someone called unrelated is no longer called copies.	Rulebook
Copies by sampled digest `copies_by_sampled_digest`	Which files go together	Files whose contents give the same fingerprint from a quick sample are grouped as holding the same bytes, as far as a sample can tell, unless a file's contents could not be read.	Rulebook
Experiments approved together `experiments_approved_together`	Which files go together	Every file beneath the experiments of a proposed group someone approved is grouped with the rest, so one yes covers the whole group.	Rulebook
Group resolved across experiments `group_resolved_across_experiments`	Which files go together	A set of words someone approves groups every experiment holding all of them, each still its own; every set asked is one some experiments share exactly, never a date or a number.	Rulebook
Group resolved within experiment `group_resolved_within_experiment`	Which files go together	Once someone approves a set of words as a group, every experiment holding that set becomes that group, each experiment (each day) its own.	Rulebook
Group series across experiments `group_series_across_experiments`	Which files go together	Once someone approves a set of words as a group, every experiment holding it stays in that set's series across the days, even when it also holds a more specific approved set.	Rulebook
Identical by content digest `identical_by_content_digest`	Which files go together	Files whose whole contents give the same fingerprint are grouped as holding the same bytes.	Rulebook
Identical by declared digest `identical_by_declared_digest`	Which files go together	Two files whose archive gives them the same checksum hold the same bytes, as the archive says it; a step below what the engine proves by reading the bytes itself, and taken back where it reads them and finds otherwise.	Rulebook
Identical by declared sha256 `identical_by_declared_sha256`	Which files go together	Two files whose archives declare one SHA-256 hold the same bytes, unless the engine's own reading of either disagrees.	Rulebook
Name family without stages `name_family_without_stages`	Which files go together	Files whose names share every word, leaving out words for the step of the work such as raw and processed, are grouped as one family of names, unless one of them is a computer's own file or a stand-in.	Rulebook
Named for a series `named_for_a_series`	Which files go together	A run of numbered files in one folder (hela_001 to hela_010) and a table beside them named for their shared name with a word saying it holds results or a summary (hela_results.xlsx) are grouped together.	Rulebook
Named for an acquisition `named_for_an_acquisition`	Which files go together	A recording from an instrument and every file whose name contains the recording's whole name, such as a table a tracking tool named after the movie it read, are grouped together, each file going with the nearest recording of that name in its experiment; so is a file whose whole name, ending included, other files' names contain (an image viewer's "movie.tif - C=0.tif"), even when it is no recording, and an image with the label, mask or annotation named after it in its folder ("vol07_labels.nii" beside "vol07.nii"), whatever step the image is at.	Rulebook
One name in sibling folders `one_name_in_sibling_folders`	Which files go together	Files with exactly the same name in folders side by side under one folder (images/a.tif and masks/a.tif) are grouped together, unless the name turns up in so many side-by-side folders that it is just how each folder names its files.	Rulebook
Replicates of one condition `replicates_of_one_condition`	Which files go together	Files in one folder whose names differ only by a counting number, such as _001 and _002, are taken as repeats of one condition; amounts with units, such as 10mM, must match in the same places, and a movie and its table are kept apart.	Rulebook
Same array shape `same_array_shape`	Which files go together	Stored arrays with the same shape, element type and storage order, in two dimensions or more, are grouped as sharing one shape.	Rulebook
Same column schema `same_column_schema`	Which files go together	Tables with the same column names in the same order and the same delimiter, two columns or more, are grouped as having the same columns, which says nothing about being one experiment.	Rulebook
Same composition `same_composition`	Which files go together	Two folders are counted as alike when the kinds of things directly inside them match and each holds at least three.	Rulebook
Same experimental condition `same_experimental_condition`	Which files go together	Files whose names give the same amounts and the same condition or reagent words are grouped as one experimental condition.	Rulebook
Same name identity `same_name_identity`	Which files go together	Files in one folder whose names match in every word, number, label, amount, date and version, with the numbers in the same places, leaving out words for the step of the work and for repeats, are grouped as one named thing, unless one of them is a computer's own file or a stand-in.	Rulebook
Same name identity within experiment `same_name_identity_within_experiment`	Which files go together	Files of one experiment whose names match in every word, number, label, amount, date and version, leaving out words for the step of the work and for repeats, are grouped as one named thing even when they sit in different folders for different steps (raw, processed, analysis), but not across folders named for different days or repeats; outside any experiment, only within one folder.	Rulebook
Same observed metadata outside programs `same_observed_metadata_outside_programs`	Which files go together	Files that match in name, size, last change and kind are grouped as probably copied from one another, except inside an installed program; whether they hold the same bytes is a separate question.	Rulebook
Same version family `same_version_family`	Which files go together	Folders whose names differ only by a version mark are grouped as versions of one thing.	Rulebook
Concerns a shared technique `concerns_a_shared_technique`	Pairs suggested for a look	Not available in this version. Two files are suggested as being about the same technique when their names mention at least two techniques in common.	Rulebook
Converted from sibling format `converted_from_sibling_format`	Pairs suggested for a look	Not available in this version. A file is suggested as a conversion of another holding the same content in a different format, when their names belong to one family.	Rulebook
Derivation by a scripts calls `derivation_by_a_scripts_calls`	Pairs suggested for a look	A file is suggested as made from another when one script's own lines read the second by name and write the first by name, which says which came first; never inside an installed program.	Rulebook
Derivation named by a describing file `derivation_named_by_a_describing_file`	Pairs suggested for a look	As shipped, suggests nothing: set to read the time, two files a script, a notebook, a log, a protocol or notes mentions would be suggested as one made from the other, the earlier first.	Rulebook
Derivation named for an acquisition `derivation_named_for_an_acquisition`	Pairs suggested for a look	A file named after a recording, or after another file's whole name, ending included, is suggested as made from it, or from the file whose whole name its own holds, whatever step its name states, and never from another file named after it by time alone; never inside an installed program.	Rulebook
Derivation of one name in sibling folders `derivation_of_one_name_in_sibling_folders`	Pairs suggested for a look	Of two files with the same name in side-by-side folders, the one in a folder whose name means raw data, images or input is suggested as the source of the one in a folder whose name means labels, masks, ground truth or output; never inside an installed program.	Rulebook
Derivation summarising a series `derivation_summarising_a_series`	Pairs suggested for a look	A table named for a run of numbered files beside it is suggested as made from each of them, one link a file, and no file of the run as made from another; never inside an installed program.	Rulebook
Derivation within name identity `derivation_within_name_identity`	Pairs suggested for a look	Two files with one name in two folders of an experiment, but for words naming a step of the work, are suggested as one made from the other, the earlier as the source, link by link, whatever step each name states; never two files of one folder, nor inside an installed program.	Rulebook
Derives from name family `derives_from_name_family`	Pairs suggested for a look	Not available in this version. A file is suggested as made from another when their names belong to one family, the first is raw data, an image made from data or a table, and at least two separate kinds of evidence agree.	Rulebook
Figure renders from tabular source `figure_renders_from_tabular_source`	Pairs suggested for a look	Not available in this version. A figure is suggested as drawn from a table of measurements or a summary whose name belongs to the same family.	Rulebook
References a mentioned file `references_a_mentioned_file`	Pairs suggested for a look	A file is suggested as pointing to another when a path it mentions leads to that file, in its own folder or elsewhere in the data, except inside an installed program.	Rulebook
Related by a describing file `related_by_a_describing_file`	Pairs suggested for a look	Two files a script, a notebook, a log, a protocol or notes mentions are suggested as related, with which, if either, was made from the other not known; never inside an installed program.	Rulebook
Related by one name in sibling folders `related_by_one_name_in_sibling_folders`	Pairs suggested for a look	Two files with the same name in side-by-side folders whose names say nothing about which came first (left/a.tif and right/a.tif) are suggested as related, with neither said to be made from the other; never inside an installed program.	Rulebook
Related within name identity `related_within_name_identity`	Pairs suggested for a look	Two files with one name in two folders of an experiment, but for words naming a step of the work, that no time puts in order, are suggested as related, with which, if either, was made from the other not known; never inside an installed program.	Rulebook
Replicates by design `replicates_by_design`	Pairs suggested for a look	Not available in this version. Two pieces of work are suggested as repeats of one another when their names give the same amounts and words and at least three separate kinds of evidence agree.	Rulebook
Succeeds by version token `succeeds_by_version_token`	Pairs suggested for a look	Not available in this version. One folder is put after another in a series of versions when both names carry a version number and they are versions of one thing.	Rulebook
Summary derives from its group `summary_derives_from_its_group`	Pairs suggested for a look	Not available in this version. A summary is suggested as made from the files of its group, when the group holds three or more files under one condition.	Rulebook
Varies in one respect `varies_in_one_respect`	Pairs suggested for a look	Not available in this version. Two pieces of work are suggested as variations of one another when their names share every word, they differ only in their condition, and at least two kinds of evidence agree.	Rulebook
Access failure is concentrated `access_failure_is_concentrated`	What is raised for attention	A folder is flagged when five or more of its files could not be read, far more often than elsewhere, or when a folder inside it could not be opened at all.	Rulebook
Binding is ambiguous outside programs `binding_is_ambiguous_outside_programs`	What is raised for attention	A file is flagged when a word in its name could mean two or more things equally and nothing tells them apart; inside an installed program, whose names are code, it is only marked.	Rulebook
Broken addresses in folder `broken_addresses_in_folder`	What is raised for attention	A folder holding files whose addresses on the archive answered not found or moved, or files with an address that could not be read as one, is flagged once, with how many, and nothing is said about whether those files exist elsewhere.	Rulebook
Claim class a person answered `claim_class_a_person_answered`	What is raised for attention	Where someone said a rule read a whole class of files wrongly (every file it gave one value), each of those readings is shown as in doubt, with their answer as the reason.	Rulebook
Clocks disagree `clocks_disagree`	What is raised for attention	Not available in this version. A file is flagged when two equally trustworthy times for it disagree by more than a day.	Rulebook
Comprehension failure is concentrated `comprehension_failure_is_concentrated`	What is raised for attention	A folder is flagged when ten or more of its files could not be made sense of, far more often than elsewhere, or when a folder inside it could not be opened at all.	Rulebook
Content contradicts extension `content_contradicts_extension`	What is raised for attention	A file is flagged when its contents begin the way one format does and its extension names another, leaving out containers such as PDF, HDF5 or ZIP that other formats are built on.	Rulebook
Content says do not analyse `content_says_do_not_analyse`	What is raised for attention	A file whose own text says "do not analyze" or "do not use" is flagged, because somebody left a note about it; nothing is skipped for it.	Rulebook
Content unreadable `content_unreadable`	What is raised for attention	A file whose contents cannot be read is flagged, saying why: it holds nothing beside siblings that hold something (an empty output), it is empty, it is empty and untouched since before a set date, it is a link the archive left in place of the file, it is a link to somewhere outside the data or to something gone, or it is not an ordinary file; inside an installed program, where empty files are ordinary, it is only marked.	Rulebook
Copied in bulk `copied_in_bulk`	What is raised for attention	A folder copied in all at once (five or more files, four in five created after they were last changed, all within ten minutes) is asked about only where its times make a later step, such as an analysis, look older than the raw data it came from.	Rulebook
Declared attribute to clarify `declared_attribute_to_clarify`	What is raised for attention	Each attribute an archive's listing states on its files is asked about once, by its name, for you to say what it means; nothing is assumed.	Rulebook
Declared copy window exceeded `declared_copy_window_exceeded`	What is raised for attention	A folder whose files an archive says were copied in over more than a day is flagged, so the one-day copy window can be adjusted.	Rulebook
Domain pack would read this pool `domain_pack_would_read_this_pool`	What is raised for attention	A subject's vocabulary pack you have not loaded would read words or file types nothing reads here, so it is offered, with how many it would read; nothing loads until you say yes.	Rulebook
Doubt in a folder name `doubt_in_a_folder_name`	What is raised for attention	A folder is flagged as in doubt when its name has a word such as wrong, failed, old, test or redo in it; a weak word, such as questionable, counts only beside another.	Rulebook
Doubt to confirm in a folder name `doubt_to_confirm_in_a_folder_name`	What is raised for attention	A folder whose name holds only weak words of doubt, such as questionable, is flagged for you to confirm.	Rulebook
Duplicate candidate unverified `duplicate_candidate_unverified`	What is raised for attention	Not available in this version. Files that look like copies of one another but whose contents were never compared are flagged for checking, except where every one sits in an organizing folder.	Rulebook
Experiments may belong together `experiments_may_belong_together`	What is raised for attention	Experiments whose folders share rare words and file names are proposed as belonging together, one question per proposed group, and nothing is grouped until someone says yes.	Rulebook
Format built on a container `format_built_on_a_container`	What is raised for attention	A file whose contents are a container, such as HDF5, is flagged as built on that container, and a ZIP under an archive's extension is asked about, since only the lab can say what it holds.	Rulebook
Group incomplete against workflow `group_incomplete_against_workflow`	What is raised for attention	Not available in this version. A group is flagged as incomplete when it has nothing at one of the steps raw, processed or analysis, naming the step that is missing.	Rulebook
Group resolution deviation `group_resolution_deviation`	What is raised for attention	Every question is a set of words some experiments share exactly, never a date or a number: the most shared first, then what each adds to a set you approved; asked word by word instead, each word added or missing is its own question.	Rulebook
Indexed label may mark replicates `indexed_label_may_mark_replicates`	What is raised for attention	A label the engine has no meaning for, numbered from 1 up to a small number and found in two or more folders, is flagged for you to say whether it marks repeats.	Rulebook
Installed software in folder `installed_software_in_folder`	What is raised for attention	A folder is recognized as an installed program, such as a copy of Fiji or a Python environment, from the parts it holds, a name ending .app, its program-style subfolders or a majority of program files; its files are still indexed and read, and rules about experiments leave them alone.	Rulebook
Miscellaneous files to approve `miscellaneous_files_to_approve`	What is raised for attention	A folder of files that is no experiment and holds none is kept as it is and offered as your miscellaneous files, for you to approve.	Rulebook
Replication below expected `replication_below_expected`	What is raised for attention	Not available in this version. A group of files under one condition is flagged when it holds fewer than three.	Rulebook
Repudiated by name `repudiated_by_name`	What is raised for attention	A file is flagged when its name says not to use it, with a word such as ignore, failed or contaminated.	Rulebook
Roi archive named but unlisted `roi_archive_named_but_unlisted`	What is raised for attention	A ZIP whose name says it holds regions of interest is flagged until a look inside lists what it holds.	Rulebook
Software outside the catalogue `software_outside_the_catalogue`	What is raised for attention	A folder laid out like a program's that no program Ingence knows matches is asked about: is it a program or not?.	Rulebook
Stage disagrees with a derivation `stage_disagrees_with_a_derivation`	What is raised for attention	Files are raised together when their names or formats put them earlier in the work than the files they were suggested as made from, one question for each folder and pair of steps.	Rulebook
Stated count may mark replicates `stated_count_may_mark_replicates`	What is raised for attention	A name stating a small count, such as N=3, is flagged: on a program or on a file past the point of recording it is read as how many things the file rests on, and on a recording, or wherever the step is unclear, as which one of several it is, for you to confirm.	Rulebook
Unbound word in a kinds place `unbound_word_in_a_kinds_place`	What is raised for attention	A word the engine has no meaning for is asked about, once for all the places it stands, where it is written in the same part of three or more names of one folder written alike as at least two words the engine knows of one kind, which are at least three quarters of the words it knows there; that kind is only a hint, and often a wrong one, so you say what the word is.	Rulebook
Vocabulary unread in folder outside programs `vocabulary_unread_in_folder_outside_programs`	What is raised for attention	A folder is flagged when more than four in five of at least twenty words in its files' names mean nothing the engine knows; inside an installed program, whose words are code, it is only marked.	Rulebook
Candidate generation is bounded `candidate_generation_is_bounded`	Limits every conclusion keeps to	At most 25 possible partners are suggested for any one file, and a file whose list was cut short is marked as such.	Rulebook
Derivation endpoints hold roles or a scripts calls `derivation_endpoints_hold_roles_or_a_scripts_calls`	Limits every conclusion keeps to	A program is never considered as made from a file, nor a file as made from a program.	Rulebook
Derivation follows the clock `derivation_follows_the_clock`	Limits every conclusion keeps to	Not available in this version. No file is counted as made from one written more than a minute after it, when both carry a trustworthy time.	Rulebook
Derivation is acyclic `derivation_is_acyclic`	Limits every conclusion keeps to	Not available in this version. No file is ever counted as made from itself, however long the chain of files in between.	Rulebook
Identity conflict blocks a derivation `identity_conflict_blocks_a_derivation`	Limits every conclusion keeps to	Two files whose names give different subjects, samples, conditions, cultures or sessions are never counted as made one from the other, whatever else they share.	Rulebook
Identity requires a content digest `identity_requires_a_content_digest`	Limits every conclusion keeps to	Not available in this version. Two files are said to hold the same bytes only when a fingerprint of their whole contents matches, never because their names, sizes or times agree.	Rulebook
Order holds within one series `order_holds_within_one_series`	Limits every conclusion keeps to	Not available in this version. Files are put in order only when they already belong to one series under the same condition.	Rulebook

Rule

A ZIP or other container holds only what opening it found, and the Index notes whether opening finished, stopped at a limit or was refused; an archive link is read from its text and never opened.

cascade.container_member · version 1

Concludes: embeds
Parameters: none
Built to run: Yes

As YAML for a project revision

This rule is provisional. It stays in force as shipped until a person confirms it, and a project revision cannot change it.

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Rule

A folder holds exactly the files, folders and bytes the walk counted inside it and beneath it.

census.directory_aggregate · version 1

Concludes: contains
Parameters: none
Built to run: Yes

As YAML for a project revision

This rule is provisional. It stays in force as shipped until a person confirms it, and a project revision cannot change it.

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Rule

A folder holds every file and folder the walk found directly inside it.

census.filesystem_containment · version 1

Concludes: contains, named directory_of
Parameters: none
Built to run: Yes

As YAML for a project revision

This rule is provisional. It stays in force as shipped until a person confirms it, and a project revision cannot change it.

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Rule

Anything on the disk that is not a file, a folder or a shortcut is recorded as what it is, such as a pipe or a device.

census.object_kind · version 1

Concludes: a recorded fact
Parameters: none
Built to run: Yes

As YAML for a project revision

This rule is provisional. It stays in force as shipped until a person confirms it, and a project revision cannot change it.

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Rule

A file in an image or electrophysiology format that an instrument writes is placed at the recording step, unless its contents contradict its extension or its own name says it was processed.

acquisition_stage_from_format · version 3+d1

Concludes: a class
Parameters: senses, written_by, concludes, minimum_match_quality, slot
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: acquisition_stage_from_format

Set its parameters, here at the shipped values

  - override: acquisition_stage_from_format
    parameters:
      senses: [image_format, ephys_format]
      written_by: [instrument]
      concludes: acquisition
      minimum_match_quality: exact
      slot: extension

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Rule

A file whose name says it holds a trajectory, which is worked out from recordings rather than recorded, is placed at the analysis step, unless it is a program.

analysis_stage_from_derived_sense · version 1+d1

Concludes: a class
Parameters: senses, concludes, minimum_match_quality, slot
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: analysis_stage_from_derived_sense

Set its parameters, here at the shipped values

  - override: analysis_stage_from_derived_sense
    parameters:
      senses: [trajectory]
      concludes: analysis
      minimum_match_quality: case_folded
      slot: name

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Rule

A file whose name carries an amount, such as 10uM or 37C, is taken to record the condition it was made under.

condition_from_quantities · version 1

Concludes: a class
Parameters: component_kinds
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: condition_from_quantities

Set its parameters, here at the shipped values

  - override: condition_from_quantities
    parameters:
      component_kinds: [quantity]

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Rule

Not available in this version. A file whose name states no condition takes the condition its folder's name states.

condition_inherited_from_folder · version 1

Concludes: a class
Parameters: theme_kind, maximum_hops
Built to run: Not yet

As YAML for a project revision

Switch it off

  - disable: condition_inherited_from_folder

Set its parameters, here at the shipped values

  - override: condition_inherited_from_folder
    parameters:
      theme_kind: condition
      maximum_hops: 1

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Rule

A date in a file's name, or else in the nearest folder name above it, says roughly when it belongs, never exactly when it was made; two dates make a span.

date_neighbourhood_of_a_file · version 1

Concludes: a class
Parameters: inherit_from_folders
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: date_neighbourhood_of_a_file

Set its parameters, here at the shipped values

  - override: date_neighbourhood_of_a_file
    parameters:
      inherit_from_folders: true

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Rule

A date in a folder's name says roughly when what it holds belongs; two dates make a span.

date_neighbourhood_of_a_folder · version 1

Concludes: a class
Parameters: inherit_from_folders
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: date_neighbourhood_of_a_folder

Set its parameters, here at the shipped values

  - override: date_neighbourhood_of_a_folder
    parameters:
      inherit_from_folders: false

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Rule

A file whose bytes the engine read under the same checksum method its archive used, and found a different checksum, does not hold what the archive said.

declared_digest_contradicted · version 1

Concludes: a class
Parameters: digest_algorithm
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: declared_digest_contradicted

Set its parameters, here at the shipped values

  - override: declared_digest_contradicted
    parameters:
      digest_algorithm: md5

Full page ›

Rule

A file whose bytes, read here, give another SHA-256 than its archive declared is marked so, and the reading here is the fact.

declared_sha256_contradicted · version 1

Concludes: a class
Parameters: digest_algorithm
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: declared_sha256_contradicted

Set its parameters, here at the shipped values

  - override: declared_sha256_contradicted
    parameters:
      digest_algorithm: sha256

Full page ›

Rule

Each file is given the earliest time it is known to have existed: a time written inside it, where one was read, and otherwise the earlier of its creation and its last change, since a copy is created after it was last changed; an impossible time, such as one from 1969 or one later than the scan that saw the file, is set aside; a document's creation date that is really the date of the blank template it was made from (midnight, years before the document was saved) is kept but not believed; where the time came from is kept with it, and a stand-in file is left out.

earliest_credible_time · version 3

Concludes: a class
Parameters: earliest_credible_year, future_tolerance_seconds, template_stamp_observers, template_stamp_minimum_gap_days
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: earliest_credible_time

Set its parameters, here at the shipped values

  - override: earliest_credible_time
    parameters:
      earliest_credible_year: 1990
      future_tolerance_seconds: 86400
      template_stamp_observers: [office, spreadsheet]
      template_stamp_minimum_gap_days: 365

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Rule

An empty file sitting among files of the same kind that hold data, such as one movie's empty tracking table beside the others' full ones, is taken as no data point and is left out when an analysis is weighed.

empty_replicate_is_no_data_point · version 3

Concludes: a class
Parameters: notes_as_names, minimum_words, note_extensions
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: empty_replicate_is_no_data_point

Set its parameters, here at the shipped values

  - override: empty_replicate_is_no_data_point
    parameters:
      notes_as_names: true
      minimum_words: 4
      note_extensions: [txt, text, md, "(none)"]

Full page ›

Rule

A folder is taken as one experiment when it holds an instrument's raw files together with files named after them, such as drift-corrected copies and results tables, and no folder above it holds the same ones, or as one session's raw files when it holds only those, or as an analysis when it holds only files named after raw files kept elsewhere, or as an analysis when it holds one program's many folders side by side, one per movie or cell, each with the same few files, all without reading what any word means.

experiment_folder_from_contents · version 3

Concludes: a class
Parameters: minimum_alike_items, most_folders_a_date, minimum_items, minimum_key_characters
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: experiment_folder_from_contents

Set its parameters, here at the shipped values

  - override: experiment_folder_from_contents
    parameters:
      minimum_alike_items: 11
      most_folders_a_date: 2
      minimum_items: 5
      minimum_key_characters: 6

Full page ›

Rule

A folder whose name holds a date beside other words is taken as an experiment, unless a folder above it already has such a name, or it is one of many folders a program wrote, one per movie or cell.

experiment_folder_from_dated_name · version 2

Concludes: a class
Parameters: none
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: experiment_folder_from_dated_name

Full page ›

Rule

A file is taken to serve the purpose its name states, such as a protocol or notes, unless it is a program or sits inside an installed program.

file_role_unless_program · version 2

Concludes: a class
Parameters: theme_kind, minimum_senses
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: file_role_unless_program

Set its parameters, here at the shipped values

  - override: file_role_unless_program
    parameters:
      theme_kind: file_role
      minimum_senses: 1

Full page ›

Rule

Files a computer makes on its own, such as .DS_Store or Thumbs.db, are recognized by how their names are spelled and set aside; an office program's lock file, whose name starts ~$, is left alone, because it means somebody was at work.

filesystem_noise_from_spelling · version 1

Concludes: a class
Parameters: senses, positions, excluded_surfaces
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: filesystem_noise_from_spelling

Set its parameters, here at the shipped values

  - override: filesystem_noise_from_spelling
    parameters:
      senses: [macos_metadata, windows_metadata, linux_metadata, editor_backup, version_control, language_cache, sync_artifact, archive_helper]
      positions: [whole, prefix, suffix]
      excluded_surfaces: ["~$"]

Full page ›

Rule

A folder whose files an archive says it received together, on one day, was copied there whole on that day; the archive's time is the copy's, never when the files were made, so nothing is put in order by it.

folder_copied_by_declared_clocks · version 1

Concludes: a class
Parameters: minimum_files, minimum_share, burst_window_seconds
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: folder_copied_by_declared_clocks

Set its parameters, here at the shipped values

  - override: folder_copied_by_declared_clocks
    parameters:
      minimum_files: 1
      minimum_share: 0.8
      burst_window_seconds: 86400

Full page ›

Rule

A folder whose files were all created within minutes of one another, after they were last changed, was copied here whole on that day, which explains its creation times and asks nothing.

folder_copied_in_bulk · version 1

Concludes: a class
Parameters: minimum_files, minimum_share, burst_window_seconds
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: folder_copied_in_bulk

Set its parameters, here at the shipped values

  - override: folder_copied_in_bulk
    parameters:
      minimum_files: 5
      minimum_share: 0.8
      burst_window_seconds: 600

Full page ›

Rule

A file is taken to be in the format its extension names, when that extension means one format and nothing else, unless its contents begin the way another format does; a container the format is built on, such as HDF5 or ZIP, does not count.

format_from_extension_unless_contradicted · version 1

Concludes: a class
Parameters: theme_kind
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: format_from_extension_unless_contradicted

Set its parameters, here at the shipped values

  - override: format_from_extension_unless_contradicted
    parameters:
      theme_kind: format

Full page ›

Rule

A file's name says it is past the point of recording when it has a word such as processed, filtered, stitched or merged in it; instrument software saves such files in its own format too.

later_stage_from_name · version 1

Concludes: a class
Parameters: theme_kind, senses, minimum_senses, minimum_match_quality
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: later_stage_from_name

Set its parameters, here at the shipped values

  - override: later_stage_from_name
    parameters:
      theme_kind: stage
      senses: [preprocessed, intermediate, processed, analysis, pooled, quantification, summary, report, export, normalised, aligned, filtered, smoothed, denoised, deconvolved, segmented, stitched, cropped, resized, downsampled, upsampled, projected, merged, masked, thresholded, binned, converted, corrected, subset, annotated]
      minimum_senses: 1
      minimum_match_quality: case_folded

Full page ›

Rule

A folder someone kept as their miscellaneous files is claimed so, and nothing in it is moved into an experiment.

miscellaneous_files_approved · version 1

Concludes: a class
Parameters: none
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: miscellaneous_files_approved

Full page ›

Rule

Not available in this version. A name is taken as typed by a person when it holds a word a machine would not write, and as written by a machine when three or more names beside it differ only by a counter.

naming_is_authored_or_emitted · version 1

Concludes: a class
Parameters: minimum_siblings
Built to run: Not yet

As YAML for a project revision

Switch it off

  - disable: naming_is_authored_or_emitted

Set its parameters, here at the shipped values

  - override: naming_is_authored_or_emitted
    parameters:
      minimum_siblings: 3

Full page ›

Rule

An empty text file whose name is a sentence is a note someone left, and its name is what it says, so it is never counted as an empty file.

note_written_as_a_file_name · version 1

Concludes: a class
Parameters: minimum_words, note_extensions
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: note_written_as_a_file_name

Set its parameters, here at the shipped values

  - override: note_written_as_a_file_name
    parameters:
      minimum_words: 4
      note_extensions: [txt, text, md, "(none)"]

Full page ›

Rule

A folder named for analysis, summaries, exports, loose files or in-between steps is taken to organize work rather than to hold one piece of it.

organising_folder_from_name · version 1

Concludes: a class
Parameters: senses
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: organising_folder_from_name

Set its parameters, here at the shipped values

  - override: organising_folder_from_name
    parameters:
      senses: [analysis, summary, export, unaffiliated, intermediate]

Full page ›

Rule

A file is placed at the step of the work its name states, such as raw, processed or analysis, unless it is a program or sits inside an installed program.

pipeline_stage_from_name · version 2

Concludes: a class
Parameters: theme_kind, senses, minimum_senses
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: pipeline_stage_from_name

Set its parameters, here at the shipped values

  - override: pipeline_stage_from_name
    parameters:
      theme_kind: stage
      senses: [raw, acquisition, preprocessed, intermediate, processed, analysis, pooled, quantification, summary, report, export]
      minimum_senses: 1

Full page ›

Rule

A shortcut, or a file that claims a size but takes up no room on the disk, is taken to stand in for contents kept somewhere else.

placeholder_from_entry_kind · version 1

Concludes: a class
Parameters: detect_stubs, minimum_declared_bytes
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: placeholder_from_entry_kind

Set its parameters, here at the shipped values

  - override: placeholder_from_entry_kind
    parameters:
      detect_stubs: true
      minimum_declared_bytes: 1

Full page ›

Rule

Files whose extensions come from programming or macro languages, such as .py, .R or an ImageJ macro, are recognized as programs, unless their contents say otherwise.

program_from_extension · version 3

Concludes: a class
Parameters: senses, minimum_match_quality, slot
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: program_from_extension

Set its parameters, here at the shipped values

  - override: program_from_extension
    parameters:
      senses: [python_source, notebook_format, shell_script, sql_source, python_wheel, python_bytecode, executable_format, c_source, c_header, javascript_source, perl_source, r_source, r_markdown, java_source, java_bytecode, fortran_module, matlab_source, imagej_macro, beanshell_script, clojure_source, ruby_source, groovy_script]
      minimum_match_quality: exact
      slot: extension

Full page ›

Rule

A file is taken to be the repeat its name numbers, such as rep2, unless it is a program.

replicate_from_indexed_label · version 1+d1

Concludes: a class
Parameters: theme_kind, minimum_match_quality
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: replicate_from_indexed_label

Set its parameters, here at the shipped values

  - override: replicate_from_indexed_label
    parameters:
      theme_kind: replicate
      minimum_match_quality: exact

Full page ›

Rule

A ZIP is recognized as a Fiji set of regions of interest when a look inside found that every item is a .roi file beginning the way Fiji's regions do, unless the ZIP is a stand-in.

roi_archive_from_members · version 1+d1

Concludes: a class
Parameters: member_extensions, header_observation, format
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: roi_archive_from_members

Set its parameters, here at the shipped values

  - override: roi_archive_from_members
    parameters:
      member_extensions: [roi]
      header_observation: "archive.imagej_roi_headers"
      format: fiji_roi_zip

Full page ›

Rule

A file whose name carries a numbered label, such as cell3, is taken to be one member of a series rather than a thing on its own.

series_member_from_index · version 1

Concludes: a class
Parameters: component_kinds
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: series_member_from_index

Set its parameters, here at the shipped values

  - override: series_member_from_index
    parameters:
      component_kinds: [indexed]

Full page ›

Rule

Not available in this version. A file whose name states no step of the work takes the step its folder's name states.

stage_inherited_from_folder · version 1

Concludes: a class
Parameters: theme_kind, maximum_hops
Built to run: Not yet

As YAML for a project revision

Switch it off

  - disable: stage_inherited_from_folder

Set its parameters, here at the shipped values

  - override: stage_inherited_from_folder
    parameters:
      theme_kind: stage
      maximum_hops: 1

Full page ›

Rule

A file is taken to be about the techniques its name mentions, when its name mentions at least two.

technique_from_name · version 1

Concludes: a class
Parameters: theme_kind, minimum_senses
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: technique_from_name

Set its parameters, here at the shipped values

  - override: technique_from_name
    parameters:
      theme_kind: technique
      minimum_senses: 2

Full page ›

Rule

A file whose name carries a version, such as v2, is taken to be one version of something rather than the whole of it.

version_from_name · version 1

Concludes: a class
Parameters: component_kinds
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: version_from_name

Set its parameters, here at the shipped values

  - override: version_from_name
    parameters:
      component_kinds: [version]

Full page ›

Rule

A link an archive left in place of a file is a copy of the file of its name held elsewhere in the folders read, matched by name and by the folders its text names; nothing is opened.

archive_link_copy_of_a_file · version 2

Concludes: equivalent
Parameters: none
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: archive_link_copy_of_a_file

Full page ›

Rule

A set of files someone called copies is grouped as copies, and a set someone called unrelated is no longer called copies.

copies_a_person_answered · version 1+d1

Concludes: equivalent
Parameters: none
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: copies_a_person_answered

Full page ›

Rule

Files whose contents give the same fingerprint from a quick sample are grouped as holding the same bytes, as far as a sample can tell, unless a file's contents could not be read.

copies_by_sampled_digest · version 1

Concludes: equivalent
Parameters: digest_algorithm
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: copies_by_sampled_digest

Set its parameters, here at the shipped values

  - override: copies_by_sampled_digest
    parameters:
      digest_algorithm: blake3_quick

Full page ›

Rule

Every file beneath the experiments of a proposed group someone approved is grouped with the rest, so one yes covers the whole group.

experiments_approved_together · version 1+d1

Concludes: equivalent
Parameters: proposal_rule
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: experiments_approved_together

Set its parameters, here at the shipped values

  - override: experiments_approved_together
    parameters:
      proposal_rule: experiments_may_belong_together

Full page ›

Rule

A set of words someone approves groups every experiment holding all of them, each still its own; every set asked is one some experiments share exactly, never a date or a number.

group_resolved_across_experiments · version 2+d1

Concludes: equivalent
Parameters: derivations, minimum_experiments, maximum_concepts, proposal_rule, term_source, acquisition_rules, minimum_word_characters, ignored_theme_kinds, minimum_core_terms
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: group_resolved_across_experiments

Set its parameters, here at the shipped values

  - override: group_resolved_across_experiments
    parameters:
      derivations: lattice
      minimum_experiments: 5
      maximum_concepts: 5000
      proposal_rule: experiments_may_belong_together
      term_source: folder_and_acquisitions
      acquisition_rules: [acquisition_stage_from_format]
      minimum_word_characters: 2
      ignored_theme_kinds: [stage, replicate, connective]
      minimum_core_terms: 2

Full page ›

Rule

Once someone approves a set of words as a group, every experiment holding that set becomes that group, each experiment (each day) its own.

group_resolved_within_experiment · version 2+d1

Concludes: equivalent
Parameters: none
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: group_resolved_within_experiment

Full page ›

Rule

Once someone approves a set of words as a group, every experiment holding it stays in that set's series across the days, even when it also holds a more specific approved set.

group_series_across_experiments · version 1+d1

Concludes: equivalent
Parameters: scale
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: group_series_across_experiments

Set its parameters, here at the shipped values

  - override: group_series_across_experiments
    parameters:
      scale: most_general

Full page ›

Rule

Files whose whole contents give the same fingerprint are grouped as holding the same bytes.

identical_by_content_digest · version 2

Concludes: identical
Parameters: digest_algorithm
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: identical_by_content_digest

Set its parameters, here at the shipped values

  - override: identical_by_content_digest
    parameters:
      digest_algorithm: blake3_whole

Full page ›

Rule

Two files whose archive gives them the same checksum hold the same bytes, as the archive says it; a step below what the engine proves by reading the bytes itself, and taken back where it reads them and finds otherwise.

identical_by_declared_digest · version 1+d1

Concludes: identical
Parameters: digest_algorithm
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: identical_by_declared_digest

Set its parameters, here at the shipped values

  - override: identical_by_declared_digest
    parameters:
      digest_algorithm: md5

Full page ›

Rule

Two files whose archives declare one SHA-256 hold the same bytes, unless the engine's own reading of either disagrees.

identical_by_declared_sha256 · version 1+d1

Concludes: identical
Parameters: digest_algorithm
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: identical_by_declared_sha256

Set its parameters, here at the shipped values

  - override: identical_by_declared_sha256
    parameters:
      digest_algorithm: sha256

Full page ›

Rule

Files whose names share every word, leaving out words for the step of the work such as raw and processed, are grouped as one family of names, unless one of them is a computer's own file or a stand-in.

name_family_without_stages · version 1+d1

Concludes: equivalent
Parameters: component_kinds, ignored_theme_kinds, minimum_components
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: name_family_without_stages

Set its parameters, here at the shipped values

  - override: name_family_without_stages
    parameters:
      component_kinds: [word]
      ignored_theme_kinds: [stage]
      minimum_components: 2

Full page ›

Rule

A run of numbered files in one folder (hela_001 to hela_010) and a table beside them named for their shared name with a word saying it holds results or a summary (hela_results.xlsx) are grouped together.

named_for_a_series · version 1+d1

Concludes: equivalent
Parameters: minimum_series_members, summary_senses, table_formats
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: named_for_a_series

Set its parameters, here at the shipped values

  - override: named_for_a_series
    parameters:
      minimum_series_members: 3
      summary_senses: [analysis, summary, quantification]
      table_formats: [tabular_format]

Full page ›

Rule

A recording from an instrument and every file whose name contains the recording's whole name, such as a table a tracking tool named after the movie it read, are grouped together, each file going with the nearest recording of that name in its experiment; so is a file whose whole name, ending included, other files' names contain (an image viewer's "movie.tif - C=0.tif"), even when it is no recording, and an image with the label, mask or annotation named after it in its folder ("vol07_labels.nii" beside "vol07.nii"), whatever step the image is at.

named_for_an_acquisition · version 2+d1

Concludes: equivalent
Parameters: minimum_key_characters, whole_name_levels_up, not_made_from_senses, annotation_senses, image_formats
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: named_for_an_acquisition

Set its parameters, here at the shipped values

  - override: named_for_an_acquisition
    parameters:
      minimum_key_characters: 6
      whole_name_levels_up: 4
      not_made_from_senses: [backup, kept_original, copy]
      annotation_senses: [annotation, annotated, masked]
      image_formats: [image_format, imaging_format]

Full page ›

Rule

Files with exactly the same name in folders side by side under one folder (images/a.tif and masks/a.tif) are grouped together, unless the name turns up in so many side-by-side folders that it is just how each folder names its files.

one_name_in_sibling_folders · version 1+d1

Concludes: equivalent
Parameters: maximum_folders, apart_folder_senses, ignored_roles, source_folder_senses, product_folder_senses
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: one_name_in_sibling_folders

Set its parameters, here at the shipped values

  - override: one_name_in_sibling_folders
    parameters:
      maximum_folders: 4
      apart_folder_senses: [cross_validation, control, treatment, wild_type, knockout]
      ignored_roles: [readme, licence, changelog, notes, metadata]
      source_folder_senses: [raw, acquisition, image, input_data]
      product_folder_senses: [annotation, annotated, masked, segmented, reference_data, analysis, processed]

Full page ›

Rule

Files in one folder whose names differ only by a counting number, such as _001 and _002, are taken as repeats of one condition; amounts with units, such as 10mM, must match in the same places, and a movie and its table are kept apart.

replicates_of_one_condition · version 1+d1

Concludes: equivalent, named same_condition_as
Parameters: compared_within, component_kinds, ignored_theme_kinds, minimum_components, ordered_component_kinds
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: replicates_of_one_condition

Set its parameters, here at the shipped values

  - override: replicates_of_one_condition
    parameters:
      compared_within: folder
      component_kinds: [word, indexed, quantity, date, version, extension]
      ignored_theme_kinds: [stage, replicate]
      minimum_components: 2
      ordered_component_kinds: [quantity]

Full page ›

Rule

Stored arrays with the same shape, element type and storage order, in two dimensions or more, are grouped as sharing one shape.

same_array_shape · version 2

Concludes: equivalent, named same_shape_as
Parameters: minimum_dimensions
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: same_array_shape

Set its parameters, here at the shipped values

  - override: same_array_shape
    parameters:
      minimum_dimensions: 2

Full page ›

Rule

Tables with the same column names in the same order and the same delimiter, two columns or more, are grouped as having the same columns, which says nothing about being one experiment.

same_column_schema · version 2

Concludes: equivalent, named same_schema_as
Parameters: minimum_columns
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: same_column_schema

Set its parameters, here at the shipped values

  - override: same_column_schema
    parameters:
      minimum_columns: 2

Full page ›

Rule

Two folders are counted as alike when the kinds of things directly inside them match and each holds at least three.

same_composition · version 1

Concludes: equivalent
Parameters: minimum_children
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: same_composition

Set its parameters, here at the shipped values

  - override: same_composition
    parameters:
      minimum_children: 3

Full page ›

Rule

Files whose names give the same amounts and the same condition or reagent words are grouped as one experimental condition.

same_experimental_condition · version 2

Concludes: equivalent, named same_condition_as
Parameters: component_kinds, counted_theme_kinds, minimum_components
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: same_experimental_condition

Set its parameters, here at the shipped values

  - override: same_experimental_condition
    parameters:
      component_kinds: [quantity, word]
      counted_theme_kinds: [condition, reagent]
      minimum_components: 1

Full page ›

Rule

Files in one folder whose names match in every word, number, label, amount, date and version, with the numbers in the same places, leaving out words for the step of the work and for repeats, are grouped as one named thing, unless one of them is a computer's own file or a stand-in.

same_name_identity · version 4+d1

Concludes: equivalent
Parameters: compared_within, component_kinds, ignored_theme_kinds, minimum_components, ordered_component_kinds
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: same_name_identity

Set its parameters, here at the shipped values

  - override: same_name_identity
    parameters:
      compared_within: folder
      component_kinds: [word, number, indexed, quantity, date, version]
      ignored_theme_kinds: [stage, replicate]
      minimum_components: 2
      ordered_component_kinds: [number, quantity]

Full page ›

Rule

Files of one experiment whose names match in every word, number, label, amount, date and version, leaving out words for the step of the work and for repeats, are grouped as one named thing even when they sit in different folders for different steps (raw, processed, analysis), but not across folders named for different days or repeats; outside any experiment, only within one folder.

same_name_identity_within_experiment · version 1+d1

Concludes: equivalent
Parameters: compared_within, ignored_subfolder_theme_kinds, component_kinds, ignored_theme_kinds, minimum_components, ordered_component_kinds
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: same_name_identity_within_experiment

Set its parameters, here at the shipped values

  - override: same_name_identity_within_experiment
    parameters:
      compared_within: experiment
      ignored_subfolder_theme_kinds: [stage]
      component_kinds: [word, number, indexed, quantity, date, version]
      ignored_theme_kinds: [stage, replicate]
      minimum_components: 2
      ordered_component_kinds: [number, quantity]

Full page ›

Rule

Files that match in name, size, last change and kind are grouped as probably copied from one another, except inside an installed program; whether they hold the same bytes is a separate question.

same_observed_metadata_outside_programs · version 2

Concludes: equivalent
Parameters: compared_facts
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: same_observed_metadata_outside_programs

Set its parameters, here at the shipped values

  - override: same_observed_metadata_outside_programs
    parameters:
      compared_facts: [name, size_bytes, modified_ns, entry_type]

Full page ›

Rule

Folders whose names differ only by a version mark are grouped as versions of one thing.

same_version_family · version 1+r4

Concludes: equivalent
Parameters: component_kinds, minimum_components
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: same_version_family

Set its parameters, here at the shipped values

  - override: same_version_family
    parameters:
      component_kinds: [word, quantity, date, number, indexed]
      minimum_components: 1

Full page ›

Rule

Not available in this version. Two files are suggested as being about the same technique when their names mention at least two techniques in common.

concerns_a_shared_technique · version 1

Concludes: concerns, named about_technique
Parameters: theme_kind, minimum_shared_senses
Built to run: Not yet

As YAML for a project revision

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  - disable: concerns_a_shared_technique

Set its parameters, here at the shipped values

  - override: concerns_a_shared_technique
    parameters:
      theme_kind: technique
      minimum_shared_senses: 2

Full page ›

Rule

Not available in this version. A file is suggested as a conversion of another holding the same content in a different format, when their names belong to one family.

converted_from_sibling_format · version 1

Concludes: derives, named converted_from
Parameters: stage_transitions
Built to run: Not yet

As YAML for a project revision

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  - disable: converted_from_sibling_format

Set its parameters, here at the shipped values

  - override: converted_from_sibling_format
    parameters:
      stage_transitions: {acquisition: raw, raw: processed}

Full page ›

Rule

A file is suggested as made from another when one script's own lines read the second by name and write the first by name, which says which came first; never inside an installed program.

derivation_by_a_scripts_calls · version 1

Concludes: derives, named processed_from
Parameters: describing_formats, minimum_resolution
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: derivation_by_a_scripts_calls

Set its parameters, here at the shipped values

  - override: derivation_by_a_scripts_calls
    parameters:
      describing_formats: [python_source, matlab_source, imagej_macro]
      minimum_resolution: unique_basename

Full page ›

Rule

As shipped, suggests nothing: set to read the time, two files a script, a notebook, a log, a protocol or notes mentions would be suggested as one made from the other, the earlier first.

derivation_named_by_a_describing_file · version 2

Concludes: derives, named processed_from
Parameters: ordered_by_time, direction, tolerance_seconds, describing_formats, minimum_resolution, describing_roles, stage_transitions
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: derivation_named_by_a_describing_file

Set its parameters, here at the shipped values

  - override: derivation_named_by_a_describing_file
    parameters:
      ordered_by_time: false
      direction: earliest_first
      tolerance_seconds: 60
      describing_formats: [python_source, r_source, r_markdown, matlab_source, shell_script, perl_source, notebook_format, imagej_macro, flowjo_workspace, log_file]
      minimum_resolution: unique_suffix
      describing_roles: [protocol, notes]
      stage_transitions: {acquisition: processed, analysis: quantification, processed: analysis, quantification: summary, raw: processed}

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Rule

A file named after a recording, or after another file's whole name, ending included, is suggested as made from it, or from the file whose whole name its own holds, whatever step its name states, and never from another file named after it by time alone; never inside an installed program.

derivation_named_for_an_acquisition · version 6

Concludes: derives, named processed_from
Parameters: link_by_link_within, tolerance_seconds, stage_transitions
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: derivation_named_for_an_acquisition

Set its parameters, here at the shipped values

  - override: derivation_named_for_an_acquisition
    parameters:
      link_by_link_within: same_name_identity_within_experiment
      tolerance_seconds: 60
      stage_transitions: {acquisition: processed, analysis: quantification, processed: analysis, quantification: summary, raw: processed}

Full page ›

Rule

Of two files with the same name in side-by-side folders, the one in a folder whose name means raw data, images or input is suggested as the source of the one in a folder whose name means labels, masks, ground truth or output; never inside an installed program.

derivation_of_one_name_in_sibling_folders · version 1

Concludes: derives, named processed_from
Parameters: direction, unless_joined_by
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: derivation_of_one_name_in_sibling_folders

Set its parameters, here at the shipped values

  - override: derivation_of_one_name_in_sibling_folders
    parameters:
      direction: directed
      unless_joined_by: [same_name_identity_within_experiment, identical_by_content_digest, copies_by_sampled_digest, identical_by_declared_digest, identical_by_declared_sha256, copies_a_person_answered, archive_link_copy_of_a_file]

Full page ›

Rule

A table named for a run of numbered files beside it is suggested as made from each of them, one link a file, and no file of the run as made from another; never inside an installed program.

derivation_summarising_a_series · version 1

Concludes: derives, named processed_from
Parameters: none
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: derivation_summarising_a_series

Full page ›

Rule

Two files with one name in two folders of an experiment, but for words naming a step of the work, are suggested as one made from the other, the earlier as the source, link by link, whatever step each name states; never two files of one folder, nor inside an installed program.

derivation_within_name_identity · version 7

Concludes: derives, named processed_from
Parameters: across_folders_only, direction, tolerance_seconds, unless_joined_by, stage_transitions
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: derivation_within_name_identity

Set its parameters, here at the shipped values

  - override: derivation_within_name_identity
    parameters:
      across_folders_only: true
      direction: earliest_first
      tolerance_seconds: 60
      unless_joined_by: named_for_an_acquisition
      stage_transitions: {acquisition: processed, analysis: quantification, processed: analysis, quantification: summary, raw: processed}

Full page ›

Rule

Not available in this version. A file is suggested as made from another when their names belong to one family, the first is raw data, an image made from data or a table, and at least two separate kinds of evidence agree.

derives_from_name_family · version 1

Concludes: derives, named processed_from
Parameters: source_roles, minimum_support
Built to run: Not yet

As YAML for a project revision

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  - disable: derives_from_name_family

Set its parameters, here at the shipped values

  - override: derives_from_name_family
    parameters:
      source_roles: [raw_acquisition, derived_image, tabular_data]
      minimum_support: 2

Full page ›

Rule

Not available in this version. A figure is suggested as drawn from a table of measurements or a summary whose name belongs to the same family.

figure_renders_from_tabular_source · version 1

Concludes: derives, named rendered_from
Parameters: stage_transitions
Built to run: Not yet

As YAML for a project revision

Switch it off

  - disable: figure_renders_from_tabular_source

Set its parameters, here at the shipped values

  - override: figure_renders_from_tabular_source
    parameters:
      stage_transitions: {quantification: figure, summary: figure}

Full page ›

Rule

A file is suggested as pointing to another when a path it mentions leads to that file, in its own folder or elsewhere in the data, except inside an installed program.

references_a_mentioned_file · version 1

Concludes: references
Parameters: minimum_resolution
Built to run: Yes

As YAML for a project revision

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  - disable: references_a_mentioned_file

Set its parameters, here at the shipped values

  - override: references_a_mentioned_file
    parameters:
      minimum_resolution: unique_suffix

Full page ›

Rule

Two files a script, a notebook, a log, a protocol or notes mentions are suggested as related, with which, if either, was made from the other not known; never inside an installed program.

related_by_a_describing_file · version 1

Concludes: concerns
Parameters: ordered_by_time, direction, tolerance_seconds, describing_formats, describing_roles, minimum_resolution
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: related_by_a_describing_file

Set its parameters, here at the shipped values

  - override: related_by_a_describing_file
    parameters:
      ordered_by_time: false
      direction: undirected
      tolerance_seconds: 60
      describing_formats: [python_source, r_source, r_markdown, matlab_source, shell_script, perl_source, notebook_format, imagej_macro, flowjo_workspace, log_file]
      describing_roles: [protocol, notes]
      minimum_resolution: unique_suffix

Full page ›

Rule

Two files with the same name in side-by-side folders whose names say nothing about which came first (left/a.tif and right/a.tif) are suggested as related, with neither said to be made from the other; never inside an installed program.

related_by_one_name_in_sibling_folders · version 1

Concludes: concerns
Parameters: direction, unless_joined_by
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: related_by_one_name_in_sibling_folders

Set its parameters, here at the shipped values

  - override: related_by_one_name_in_sibling_folders
    parameters:
      direction: undirected
      unless_joined_by: [same_name_identity_within_experiment, identical_by_content_digest, copies_by_sampled_digest, identical_by_declared_digest, identical_by_declared_sha256, copies_a_person_answered, archive_link_copy_of_a_file]

Full page ›

Rule

Two files with one name in two folders of an experiment, but for words naming a step of the work, that no time puts in order, are suggested as related, with which, if either, was made from the other not known; never inside an installed program.

related_within_name_identity · version 3

Concludes: concerns
Parameters: across_folders_only, direction, tolerance_seconds, unless_joined_by
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: related_within_name_identity

Set its parameters, here at the shipped values

  - override: related_within_name_identity
    parameters:
      across_folders_only: true
      direction: undirected
      tolerance_seconds: 60
      unless_joined_by: named_for_an_acquisition

Full page ›

Rule

Not available in this version. Two pieces of work are suggested as repeats of one another when their names give the same amounts and words and at least three separate kinds of evidence agree.

replicates_by_design · version 1

Concludes: equivalent, named replicate_of
Parameters: agreeing_kinds, minimum_support, requires_repeat_marker
Built to run: Not yet

As YAML for a project revision

Switch it off

  - disable: replicates_by_design

Set its parameters, here at the shipped values

  - override: replicates_by_design
    parameters:
      agreeing_kinds: [quantity, word]
      minimum_support: 3
      requires_repeat_marker: false

Full page ›

Rule

Not available in this version. One folder is put after another in a series of versions when both names carry a version number and they are versions of one thing.

succeeds_by_version_token · version 1

Concludes: succeeds, named version_of
Parameters: ordering_kind, series_equivalence
Built to run: Not yet

As YAML for a project revision

Switch it off

  - disable: succeeds_by_version_token

Set its parameters, here at the shipped values

  - override: succeeds_by_version_token
    parameters:
      ordering_kind: version
      series_equivalence: version_family

Full page ›

Rule

Not available in this version. A summary is suggested as made from the files of its group, when the group holds three or more files under one condition.

summary_derives_from_its_group · version 1

Concludes: derives, named summarized_from
Parameters: member_respect, minimum_members
Built to run: Not yet

As YAML for a project revision

Switch it off

  - disable: summary_derives_from_its_group

Set its parameters, here at the shipped values

  - override: summary_derives_from_its_group
    parameters:
      member_respect: experimental_condition
      minimum_members: 3

Full page ›

Rule

Not available in this version. Two pieces of work are suggested as variations of one another when their names share every word, they differ only in their condition, and at least two kinds of evidence agree.

varies_in_one_respect · version 1

Concludes: equivalent, named variant_of
Parameters: agreeing_kinds, varying_respect, minimum_support
Built to run: Not yet

As YAML for a project revision

Switch it off

  - disable: varies_in_one_respect

Set its parameters, here at the shipped values

  - override: varies_in_one_respect
    parameters:
      agreeing_kinds: [word]
      varying_respect: experimental_condition
      minimum_support: 2

Full page ›

Rule

A folder is flagged when five or more of its files could not be read, far more often than elsewhere, or when a folder inside it could not be opened at all.

access_failure_is_concentrated · version 2

Concludes: a finding
Parameters: failure_class, minimum_failures, concentration_factor
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: access_failure_is_concentrated

Set its parameters, here at the shipped values

  - override: access_failure_is_concentrated
    parameters:
      failure_class: access
      minimum_failures: 5
      concentration_factor: 3.0

Full page ›

Rule

A file is flagged when a word in its name could mean two or more things equally and nothing tells them apart; inside an installed program, whose names are code, it is only marked.

binding_is_ambiguous_outside_programs · version 1

Concludes: a finding
Parameters: reading, minimum_alternatives
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: binding_is_ambiguous_outside_programs

Set its parameters, here at the shipped values

  - override: binding_is_ambiguous_outside_programs
    parameters:
      reading: dictionary_binding
      minimum_alternatives: 2

Full page ›

Rule

A folder holding files whose addresses on the archive answered not found or moved, or files with an address that could not be read as one, is flagged once, with how many, and nothing is said about whether those files exist elsewhere.

broken_addresses_in_folder · version 1+d1

Concludes: a finding
Parameters: minimum_files
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: broken_addresses_in_folder

Set its parameters, here at the shipped values

  - override: broken_addresses_in_folder
    parameters:
      minimum_files: 1

Full page ›

Rule

Where someone said a rule read a whole class of files wrongly (every file it gave one value), each of those readings is shown as in doubt, with their answer as the reason.

claim_class_a_person_answered · version 1+d1

Concludes: a finding
Parameters: none
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: claim_class_a_person_answered

Full page ›

Rule

Not available in this version. A file is flagged when two equally trustworthy times for it disagree by more than a day.

clocks_disagree · version 1+d1

Concludes: a finding
Parameters: reading, tolerance_seconds
Built to run: Not yet

As YAML for a project revision

Switch it off

  - disable: clocks_disagree

Set its parameters, here at the shipped values

  - override: clocks_disagree
    parameters:
      reading: event_time
      tolerance_seconds: 86400

Full page ›

Rule

A folder is flagged when ten or more of its files could not be made sense of, far more often than elsewhere, or when a folder inside it could not be opened at all.

comprehension_failure_is_concentrated · version 2

Concludes: a finding
Parameters: failure_class, minimum_failures, concentration_factor
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: comprehension_failure_is_concentrated

Set its parameters, here at the shipped values

  - override: comprehension_failure_is_concentrated
    parameters:
      failure_class: comprehension
      minimum_failures: 10
      concentration_factor: 5.0

Full page ›

Rule

A file is flagged when its contents begin the way one format does and its extension names another, leaving out containers such as PDF, HDF5 or ZIP that other formats are built on.

content_contradicts_extension · version 1+d1

Concludes: a finding
Parameters: detector, raises, container_media_types, unclear_media_types
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: content_contradicts_extension

Set its parameters, here at the shipped values

  - override: content_contradicts_extension
    parameters:
      detector: signature
      raises: contradiction
      container_media_types: ["application/gzip", "application/pdf", "application/x-hdf5", "application/x-ole-storage", "application/x-tar", "application/x-xz", "application/x-bzip2", "application/vnd.sqlite3", "application/x-iso9660-image", "application/x-elf", "application/x-mach-binary", "video/mp4", "video/quicktime"]
      unclear_media_types: ["application/zip"]

Full page ›

Rule

A file whose own text says "do not analyze" or "do not use" is flagged, because somebody left a note about it; nothing is skipped for it.

content_says_do_not_analyse · version 1+d1

Concludes: a finding
Parameters: phrases
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: content_says_do_not_analyse

Set its parameters, here at the shipped values

  - override: content_says_do_not_analyse
    parameters:
      phrases: [donotanalyse, "do-not-analyse", do_not_analyse, donotanalyze, "do-not-analyze", do_not_analyze, notforanalysis, excludefromanalysis, donotuse, "do-not-use", do_not_use]

Full page ›

Rule

A file whose contents cannot be read is flagged, saying why: it holds nothing beside siblings that hold something (an empty output), it is empty, it is empty and untouched since before a set date, it is a link the archive left in place of the file, it is a link to somewhere outside the data or to something gone, or it is not an ordinary file; inside an installed program, where empty files are ordinary, it is only marked.

content_unreadable · version 7

Concludes: a finding
Parameters: notes_as_names, minimum_words, note_extensions, written_before
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: content_unreadable

Set its parameters, here at the shipped values

  - override: content_unreadable
    parameters:
      notes_as_names: true
      minimum_words: 4
      note_extensions: [txt, text, md, "(none)"]
      written_before: "2025-09-16T00:00:00Z"

Full page ›

Rule

A folder copied in all at once (five or more files, four in five created after they were last changed, all within ten minutes) is asked about only where its times make a later step, such as an analysis, look older than the raw data it came from.

copied_in_bulk · version 2+d1

Concludes: a finding
Parameters: minimum_files, minimum_share, burst_window_seconds, stage_rules, entry_stages, time_rule
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: copied_in_bulk

Set its parameters, here at the shipped values

  - override: copied_in_bulk
    parameters:
      minimum_files: 5
      minimum_share: 0.8
      burst_window_seconds: 600
      stage_rules: [acquisition_stage_from_format, pipeline_stage_from_name, analysis_stage_from_derived_sense]
      entry_stages: [raw, acquisition]
      time_rule: earliest_credible_time

Full page ›

Rule

Each attribute an archive's listing states on its files is asked about once, by its name, for you to say what it means; nothing is assumed.

declared_attribute_to_clarify · version 1+d1

Concludes: a finding
Parameters: none
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: declared_attribute_to_clarify

Full page ›

Rule

A folder whose files an archive says were copied in over more than a day is flagged, so the one-day copy window can be adjusted.

declared_copy_window_exceeded · version 1+d1

Concludes: a finding
Parameters: minimum_files, minimum_share, burst_window_seconds
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: declared_copy_window_exceeded

Set its parameters, here at the shipped values

  - override: declared_copy_window_exceeded
    parameters:
      minimum_files: 2
      minimum_share: 0.8
      burst_window_seconds: 86400

Full page ›

Rule

A subject's vocabulary pack you have not loaded would read words or file types nothing reads here, so it is offered, with how many it would read; nothing loads until you say yes.

domain_pack_would_read_this_pool · version 4

Concludes: a finding
Parameters: minimum_files, minimum_spellings, minimum_share, share_of, asked_first
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: domain_pack_would_read_this_pool

Set its parameters, here at the shipped values

  - override: domain_pack_would_read_this_pool
    parameters:
      minimum_files: 3
      minimum_spellings: 3
      minimum_share: 0.02
      share_of: either
      asked_first: true

Full page ›

Rule

A folder is flagged as in doubt when its name has a word such as wrong, failed, old, test or redo in it; a weak word, such as questionable, counts only beside another.

doubt_in_a_folder_name · version 1+d1

Concludes: a finding
Parameters: raises, minimum_terms, senses, low_strength_senses
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: doubt_in_a_folder_name

Set its parameters, here at the shipped values

  - override: doubt_in_a_folder_name
    parameters:
      raises: doubt
      minimum_terms: 1
      senses: [wrong, bad, broken, invalid, failed, contaminated, do_not_use, ignore, deprecated, obsolete, delete, archive_only, temporary, scratch, test_artifact, debug, dummy, example, final_final, use_this_one, version_soup, emphatic, untitled, default_name, new_folder, keyboard_mash, questionable, unsure, check, fixme, todo, redo, recovered, conflicted, duplicate, excluded, quarantine, superseded_by]
      low_strength_senses: [keyboard_mash, questionable, quarantine]

Full page ›

Rule

A folder whose name holds only weak words of doubt, such as questionable, is flagged for you to confirm.

doubt_to_confirm_in_a_folder_name · version 1+d1

Concludes: a finding
Parameters: raises, minimum_terms, senses, low_strength_senses
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: doubt_to_confirm_in_a_folder_name

Set its parameters, here at the shipped values

  - override: doubt_to_confirm_in_a_folder_name
    parameters:
      raises: confirmation
      minimum_terms: 1
      senses: [wrong, bad, broken, invalid, failed, contaminated, do_not_use, ignore, deprecated, obsolete, delete, archive_only, temporary, scratch, test_artifact, debug, dummy, example, final_final, use_this_one, version_soup, emphatic, untitled, default_name, new_folder, keyboard_mash, questionable, unsure, check, fixme, todo, redo, recovered, conflicted, duplicate, excluded, quarantine, superseded_by]
      low_strength_senses: [keyboard_mash, questionable, quarantine]

Full page ›

Rule

Not available in this version. Files that look like copies of one another but whose contents were never compared are flagged for checking, except where every one sits in an organizing folder.

duplicate_candidate_unverified · version 1+d1

Concludes: a finding
Parameters: member_respect, minimum_members, ignore_organising_folders
Built to run: Not yet

As YAML for a project revision

Switch it off

  - disable: duplicate_candidate_unverified

Set its parameters, here at the shipped values

  - override: duplicate_candidate_unverified
    parameters:
      member_respect: observed_metadata
      minimum_members: 2
      ignore_organising_folders: true

Full page ›

Rule

Experiments whose folders share rare words and file names are proposed as belonging together, one question per proposed group, and nothing is grouped until someone says yes.

experiments_may_belong_together · version 3+d1

Concludes: a finding
Parameters: ignored_theme_kinds, experiment_rules, policy, neighbours, minimum_similarity, minimum_shared, maximum_group_size, maximum_groups, common_share
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: experiments_may_belong_together

Set its parameters, here at the shipped values

  - override: experiments_may_belong_together
    parameters:
      ignored_theme_kinds: [stage, replicate, connective]
      experiment_rules: [experiment_folder_from_contents, experiment_folder_from_dated_name]
      policy: name_first
      neighbours: 3
      minimum_similarity: 0.2
      minimum_shared: 2
      maximum_group_size: 8
      maximum_groups: 0
      common_share: 0.25

Full page ›

Rule

A file whose contents are a container, such as HDF5, is flagged as built on that container, and a ZIP under an archive's extension is asked about, since only the lab can say what it holds.

format_built_on_a_container · version 2+d1

Concludes: a finding
Parameters: detector, raises, container_media_types, unclear_media_types, archive_types
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: format_built_on_a_container

Set its parameters, here at the shipped values

  - override: format_built_on_a_container
    parameters:
      detector: signature
      raises: container
      container_media_types: ["application/gzip", "application/pdf", "application/x-hdf5", "application/x-ole-storage", "application/x-tar", "application/x-xz", "application/x-bzip2", "application/vnd.sqlite3", "application/x-iso9660-image", "application/x-elf", "application/x-mach-binary", "video/mp4", "video/quicktime"]
      unclear_media_types: ["application/zip"]
      archive_types: [archive_format, compressed_archive, compression_format]

Full page ›

Rule

Not available in this version. A group is flagged as incomplete when it has nothing at one of the steps raw, processed or analysis, naming the step that is missing.

group_incomplete_against_workflow · version 1+d1

Concludes: a finding
Parameters: required_stages
Built to run: Not yet

As YAML for a project revision

Switch it off

  - disable: group_incomplete_against_workflow

Set its parameters, here at the shipped values

  - override: group_incomplete_against_workflow
    parameters:
      required_stages: [raw, processed, analysis]

Full page ›

Rule

Every question is a set of words some experiments share exactly, never a date or a number: the most shared first, then what each adds to a set you approved; asked word by word instead, each word added or missing is its own question.

group_resolution_deviation · version 2

Concludes: a finding
Parameters: asked_first
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: group_resolution_deviation

Set its parameters, here at the shipped values

  - override: group_resolution_deviation
    parameters:
      asked_first: true

Full page ›

Rule

A label the engine has no meaning for, numbered from 1 up to a small number and found in two or more folders, is flagged for you to say whether it marks repeats.

indexed_label_may_mark_replicates · version 1+d1

Concludes: a finding
Parameters: maximum_index, minimum_folders
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: indexed_label_may_mark_replicates

Set its parameters, here at the shipped values

  - override: indexed_label_may_mark_replicates
    parameters:
      maximum_index: 9
      minimum_folders: 2

Full page ›

Rule

A folder is recognized as an installed program, such as a copy of Fiji or a Python environment, from the parts it holds, a name ending .app, its program-style subfolders or a majority of program files; its files are still indexed and read, and rules about experiments leave them alone.

installed_software_in_folder · version 3

Concludes: a finding
Parameters: archive_suffixes, minimum_code_share, bundle_name_suffixes, layout_folder_names, minimum_layout_folders, program_extensions, minimum_program_files, minimum_program_share, manifest_names
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: installed_software_in_folder

Set its parameters, here at the shipped values

  - override: installed_software_in_folder
    parameters:
      archive_suffixes: [".zip", ".tar.gz", ".tgz", ".tar.bz2", ".tar.xz", ".tar"]
      minimum_code_share: 0.5
      bundle_name_suffixes: [".app"]
      layout_folder_names: [bin, sbin, lib, lib64, libexec, include, share, "site-packages", "dist-packages", Frameworks, __pycache__, node_modules]
      minimum_layout_folders: 2
      program_extensions: [h, hpp, so, dylib, dll, a, o, lib, pyc, pyd, class, jar, exe]
      minimum_program_files: 20
      minimum_program_share: 0.5
      manifest_names: ["setup.py", "setup.cfg", "pyproject.toml", "package.json", "CMakeLists.txt", Makefile, configure, "Cargo.toml"]

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Rule

A folder of files that is no experiment and holds none is kept as it is and offered as your miscellaneous files, for you to approve.

miscellaneous_files_to_approve · version 2

Concludes: a finding
Parameters: experiment_rules, minimum_files, minimum_outside_share, organising_folders, minimum_experiments_held
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: miscellaneous_files_to_approve

Set its parameters, here at the shipped values

  - override: miscellaneous_files_to_approve
    parameters:
      experiment_rules: [experiment_folder_from_contents, experiment_folder_from_dated_name]
      minimum_files: 2
      minimum_outside_share: 0.5
      organising_folders: false
      minimum_experiments_held: 2

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Rule

Not available in this version. A group of files under one condition is flagged when it holds fewer than three.

replication_below_expected · version 1+d1

Concludes: a finding
Parameters: expected_members, member_respect
Built to run: Not yet

As YAML for a project revision

Switch it off

  - disable: replication_below_expected

Set its parameters, here at the shipped values

  - override: replication_below_expected
    parameters:
      expected_members: 3
      member_respect: experimental_condition

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Rule

A file is flagged when its name says not to use it, with a word such as ignore, failed or contaminated.

repudiated_by_name · version 1+d1

Concludes: a finding
Parameters: senses, minimum_terms
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: repudiated_by_name

Set its parameters, here at the shipped values

  - override: repudiated_by_name
    parameters:
      senses: [do_not_use, ignore, deprecated, delete, wrong, broken, failed, contaminated]
      minimum_terms: 1

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Rule

A ZIP whose name says it holds regions of interest is flagged until a look inside lists what it holds.

roi_archive_named_but_unlisted · version 1+d1

Concludes: a finding
Parameters: archive_senses, named_senses
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: roi_archive_named_but_unlisted

Set its parameters, here at the shipped values

  - override: roi_archive_named_but_unlisted
    parameters:
      archive_senses: [archive_format]
      named_senses: [region_of_interest]

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Rule

A folder laid out like a program's that no program Ingence knows matches is asked about: is it a program or not?.

software_outside_the_catalogue · version 1+d1

Concludes: a finding
Parameters: layout_folder_names, program_extensions, marker_names, bundle_name_suffixes, minimum_evidence
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: software_outside_the_catalogue

Set its parameters, here at the shipped values

  - override: software_outside_the_catalogue
    parameters:
      layout_folder_names: [bin, sbin, lib, lib64, libexec, include, plugins, jars, Frameworks, "site-packages"]
      program_extensions: [so, dylib, dll, a, o, lib, pyd, class, jar, exe, h, hpp]
      marker_names: [license, licence, copying, version, changelog]
      bundle_name_suffixes: [".app"]
      minimum_evidence: 2

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Rule

Files are raised together when their names or formats put them earlier in the work than the files they were suggested as made from, one question for each folder and pair of steps.

stage_disagrees_with_a_derivation · version 2+d1

Concludes: a finding
Parameters: stage_transitions
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: stage_disagrees_with_a_derivation

Set its parameters, here at the shipped values

  - override: stage_disagrees_with_a_derivation
    parameters:
      stage_transitions: {acquisition: processed, analysis: quantification, processed: analysis, quantification: summary, raw: processed}

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Rule

A name stating a small count, such as N=3, is flagged: on a program or on a file past the point of recording it is read as how many things the file rests on, and on a recording, or wherever the step is unclear, as which one of several it is, for you to confirm.

stated_count_may_mark_replicates · version 2+d1

Concludes: a finding
Parameters: maximum_count, theme_kind, stage_rules, observation_rules, derivation_rules
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: stated_count_may_mark_replicates

Set its parameters, here at the shipped values

  - override: stated_count_may_mark_replicates
    parameters:
      maximum_count: 9
      theme_kind: count
      stage_rules: [pipeline_stage_from_name, acquisition_stage_from_format, analysis_stage_from_derived_sense]
      observation_rules: [acquisition_stage_from_format]
      derivation_rules: [program_from_extension]

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Rule

A word the engine has no meaning for is asked about, once for all the places it stands, where it is written in the same part of three or more names of one folder written alike as at least two words the engine knows of one kind, which are at least three quarters of the words it knows there; that kind is only a hint, and often a wrong one, so you say what the word is.

unbound_word_in_a_kinds_place · version 1

Concludes: a finding
Parameters: minimum_bound, agreement, minimum_names
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: unbound_word_in_a_kinds_place

Set its parameters, here at the shipped values

  - override: unbound_word_in_a_kinds_place
    parameters:
      minimum_bound: 2
      agreement: 0.75
      minimum_names: 3

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Rule

A folder is flagged when more than four in five of at least twenty words in its files' names mean nothing the engine knows; inside an installed program, whose words are code, it is only marked.

vocabulary_unread_in_folder_outside_programs · version 1

Concludes: a finding
Parameters: denominator, maximum_unbound_share, minimum_occurrences
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: vocabulary_unread_in_folder_outside_programs

Set its parameters, here at the shipped values

  - override: vocabulary_unread_in_folder_outside_programs
    parameters:
      denominator: word_occurrences
      maximum_unbound_share: 0.8
      minimum_occurrences: 20

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Rule

At most 25 possible partners are suggested for any one file, and a file whose list was cut short is marked as such.

candidate_generation_is_bounded · version 1

Concludes: a limit
Parameters: maximum_candidates
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: candidate_generation_is_bounded

Set its parameters, here at the shipped values

  - override: candidate_generation_is_bounded
    parameters:
      maximum_candidates: 25

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Rule

A program is never considered as made from a file, nor a file as made from a program.

derivation_endpoints_hold_roles_or_a_scripts_calls · version 2

Concludes: derives
Parameters: excluded_classes
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: derivation_endpoints_hold_roles_or_a_scripts_calls

Set its parameters, here at the shipped values

  - override: derivation_endpoints_hold_roles_or_a_scripts_calls
    parameters:
      excluded_classes: [python_source, notebook_format, shell_script, sql_source, python_wheel, python_bytecode, executable_format, c_source, c_header, javascript_source, perl_source, r_source, r_markdown, java_source, java_bytecode, fortran_module, matlab_source, imagej_macro, beanshell_script, clojure_source, ruby_source, groovy_script]

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Rule

Not available in this version. No file is counted as made from one written more than a minute after it, when both carry a trustworthy time.

derivation_follows_the_clock · version 1

Concludes: derives
Parameters: minimum_clock_tier, tolerance_seconds
Built to run: Not yet

As YAML for a project revision

Switch it off

  - disable: derivation_follows_the_clock

Set its parameters, here at the shipped values

  - override: derivation_follows_the_clock
    parameters:
      minimum_clock_tier: document
      tolerance_seconds: 60

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Rule

Not available in this version. No file is ever counted as made from itself, however long the chain of files in between.

derivation_is_acyclic · version 1

Concludes: derives
Parameters: max_chain_length
Built to run: Not yet

As YAML for a project revision

Switch it off

  - disable: derivation_is_acyclic

Set its parameters, here at the shipped values

  - override: derivation_is_acyclic
    parameters:
      max_chain_length: 64

Full page ›

Rule

Two files whose names give different subjects, samples, conditions, cultures or sessions are never counted as made one from the other, whatever else they share.

identity_conflict_blocks_a_derivation · version 1

Concludes: derives
Parameters: identity_bearing_kinds
Built to run: Yes

As YAML for a project revision

Switch it off

  - disable: identity_conflict_blocks_a_derivation

Set its parameters, here at the shipped values

  - override: identity_conflict_blocks_a_derivation
    parameters:
      identity_bearing_kinds: [subject, sample, condition, culture, session]

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Rule

Not available in this version. Two files are said to hold the same bytes only when a fingerprint of their whole contents matches, never because their names, sizes or times agree.

identity_requires_a_content_digest · version 1

Concludes: identical
Parameters: permitted_methods
Built to run: Not yet

As YAML for a project revision

Switch it off

  - disable: identity_requires_a_content_digest

Set its parameters, here at the shipped values

  - override: identity_requires_a_content_digest
    parameters:
      permitted_methods: [content_full]

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Rule

Not available in this version. Files are put in order only when they already belong to one series under the same condition.

order_holds_within_one_series · version 1

Concludes: succeeds
Parameters: series_equivalence
Built to run: Not yet

As YAML for a project revision

Switch it off

  - disable: order_holds_within_one_series

Set its parameters, here at the shipped values

  - override: order_holds_within_one_series
    parameters:
      series_equivalence: experimental_condition

Full page ›

Copy what Ingence reads#

Each entry has a Copy button. It puts on your clipboard text that Ingence reads as it stands. The same text is under “As YAML” on every card, to select by hand.

A word copies as an entry of a pack file. Paste it under entries: in a pack of your own, change the spellings to the ones your laboratory writes, and install the pack with ingence teach pack install. Writing a pack shows the whole file. Every word shown is already in your Dictionary, so a copied entry is a starting point for your own spelling or meaning in your own pack, and pasting it unchanged makes a tie that the engine reports.
A rule copies as a change to put in your project’s own revision file, in the project’s rulebook folder. One change switches the rule off. The other sets the rule’s parameters, here at their shipped values. Paste either under changes:. A provisional rule has neither, because it stays in force as shipped until a person confirms it.

A revision file that switches one rule off looks like this:

project_revision: 1
summary: Switch off one rule.
changes:
  - disable: copied_in_bulk

A rule set at other values looks like this. The rule reads the new value from the next run.

project_revision: 2
summary: Ask about smaller folders copied in bulk.
changes:
  - override: copied_in_bulk
    parameters:
      minimum_files: 3

A setting copies from the settings page as the lines of settings.yaml that hold it.