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v0.4.0
BioDataLink 0.4.0 adds reusable scientific plots and develops eleven tutorials into visual computational essays, with a new essay on sampling and uncertainty. The essays use repeated experiments, controls, sensitivity checks and short interpretations around computed figures.
BioEmbeddingPlot: align coordinates and annotations by observation ID.BioExpressionDotPlot: show group means and detection fractions from dense or sparse measurements.BioSequenceCompositionPlotandBioSequenceSkewPlot: inspect DNA word counts and windowed base composition with explicit ambiguity handling.BioStructureComparisonPlot: align residue-keyed traces by a selected region, preserving units and handedness.
The essays cover single-cell expression, protein conformations, sequence composition, circadian rhythms, geometry, networks, discretization, sparse measurements, prediction and model discrimination. The new sampling essay compares bootstrap and permutation experiments, measurement error and selective missingness using the bundled Iris data.
Includes 38 documentation notebooks, five new symbol references and a visualization guide. Requires Wolfram Language 15.0 or later.
Computational essays · Visualization guide · Changelog
The attached archive comes from successful main-branch CI for commit 975e533cf5dd9d6705ace2f617c47bca1c62cabb. Wolfram Cloud builds and publishes from the same released commit.
v0.3.7
v0.3.6
v0.3.5
v0.3.4
v0.3.3
v0.3.2
v0.3.1
BioDataLink 0.3.1 simplifies the documentation while preserving the scientific computations and figures.
- Shorter Wolfram Language examples across eleven tutorials and eight reference pages.
- Tutorial helpers appear in a final Initialization section and run as native initialization cells.
- Focused option examples and readable comparison scales.
- A concise README and documentation skills that carry these conventions forward.
Install the current published resource:
PacletInstall[ResourceObject["https://wolfr.am/1IzdEvymT"]]
Needs["WolframInstitute`BioDataLink`"]Documentation · Wolfram resource
The GitHub asset is the archive verified by CI. Wolfram Cloud publishes the same source commit and version through the dependent publication workflow.
v0.3.0
BioDataLink 0.3.0 connects biological data to Wolfram Language 15.0 and later.
Documentation · Wolfram Cloud resource
Install from the published Cloud resource:
PacletInstall[ResourceObject["https://wolfr.am/1IzdEvymT"]]
Needs["WolframInstitute`BioDataLink`"]- Discover sources in a bundled Identifiers.org directory and construct accession links.
- Search public BioStudies and GEO study metadata with explicit pagination.
- Browse metadata for 55 Pertpy loader entries.
- Download selected HTTPS files with byte limits and optional size and SHA-256 checks.
- Read the BioDataLink JSON interchange format or selected H5AD matrices with aligned metadata and sparse storage.
- Work through eleven tutorials covering data access, measurement geometry, sparse data, finite-state encodings, predictive rules, similarity graphs, cellular automata and measurement selection.
HTTPS downloads require curl 8.4 or later. H5AD support requires an explicitly configured Python interpreter with h5py and NumPy. BioDataLink does not install those optional dependencies automatically.
Source-directory entries do not establish open access or reader support. Private-data access is not part of this release. Examples distinguish measured data from synthetic inputs and model predictions from biological mechanisms.
The GitHub archives come from the successful CI run for the tagged commit. The versioned archive supports reproducible installations. Cloud publication rebuilt the paclet from the same tagged commit and verified the public site.
Code is MIT licensed. Bundled registry and Iris data retain their CC BY 4.0 attribution. Cite the original data sources used in your research.