19 projects
scigantic-headers
Decode scientific file headers (cryo-EM, light microscopy and light-sheet imaging incl. TIFF/OME-TIFF, CZI, HDF5/Imaris/BigDataViewer, LIF, ND2, Zarr/N5; tabular, flow cytometry, mass spec, sequencing, structural biology) into typed fields. Pure, zero-dependency, with bounded readers that follow internal pointers without downloading the file.
scigantic-bil
Search the Brain Image Library (14,000+ BICCN/BICAN brain microscopy datasets, 6 PB) and read light-sheet, fMOST, STPT and tracing volumes (TIFF, OME-TIFF, JPEG 2000, OME-Zarr) over HTTP without downloading them: a typed catalog over BIL's daily inventory and metadata API, lazy file listing, single-slice TIFF reads, thumbnails, OME-Zarr access, and BIL's BrAinPI OME-Zarr and Neuroglancer views.
scigantic-wwpdb
The wwPDB Chemical Component Dictionary (CCD), by id, no download.
scigantic-ucsc
Read UCSC Genome Browser conservation scores, multiz alignments, TOGA gene annotations and assembly lists straight from UCSC's public S3 bucket, without downloading the files.
scigantic-cards
A small data card format and linter for LLM agents: record what differs from the well-known dataset, how big it is, and how to open it.
scigantic-empiar
Explore the EMPIAR cryo-EM archive from Python — stream any of ~3,000 datasets (8.9 PiB) over parallel HTTP range reads, nothing downloaded.
scigantic-emdb
Search every structure in EMDB from Python — 60,895 cryo-EM maps by protein, organism, resolution, molecular weight and PDB cross-reference, then read one in two calls.
scigantic-facebase
Search FaceBase, the craniofacial research data hub, and read its open-access micro-CT, imaging and sequencing data from Python: a typed catalog over FaceBase's open metadata API, citations in the form its Terms of Use ask for, ranged reads of remote files, and single-slice reads from zipped micro-CT stacks without downloading them.
scigantic-nci
Analysis-ready NCI cancer data in one import: per-project GDC tables (clinical, RNA-Seq, mutations, copy number, miRNA, RPPA, methylation) and per-collection Imaging Data Commons indexes with sample DICOM, read from public S3 or a mounted copy. No account, no download step, no BigQuery.
scigantic-pubchem
Query PubChem live via PUG REST, with rate-limit-aware retry, expiring cache, live similarity/substructure/cross-reference search, bioassay/gene/protein/PDB cross-reference data (with a streaming downloader, and a resumable raw dose-response Data Table reader for qHTS assays), the Tox21 Data Challenge panel, and CID-keyed reads of a local parquet mirror of the identifier/name/mass registry.
scigantic-chembl
Query ChEMBL directly from a public S3 mirror with DuckDB, including a pre-joined potency table, similarity search, and substructure search.
scigantic-comptox
Query EPA's CompTox Chemicals Dashboard: ToxCast bioactivity (winning dose-response model + hit-call per chemical/assay-endpoint) from a public S3 mirror, plus live Chemical/Hazard/Exposure lookups via EPA's CCTE API.
scigantic-bindingdb
Query BindingDB directly from a public S3 mirror with DuckDB, including a ChEMBL cross-reference bridge table and a ready drug-target-interaction training table.
scigantic-who
Query every WHO Global Health Observatory indicator from a public parquet mirror over DuckDB (one query instead of 3,099 API calls), decode WHO's dimension codes, or fetch a fresh indicator from the live OData API in the same shape.
scigantic-surechembl
SureChEMBL patent chemistry from Python: compounds by id, name, SMILES or InChIKey, structure search, patents by compound, Solr full-text search, full patent documents with their extracted chemistry, DOCDB families, ChEMBL/PubChem/DrugBank/ChEBI/PDB/BindingDB cross-references via UniChem, the bulk parquet releases read in place from EBI with DuckDB, and joins into scigantic-chembl, scigantic-bindingdb and scigantic-pubchem. No mirror, no download, no key.
scigantic-mcp
MCP server for the Scigantic catalog of public scientific data archives, with LLM-ready schema cards, plus SureChEMBL patent chemistry tools
scigantic-deeppk
Client for Deep-PK's small-molecule ADMET/toxicity prediction API, plus a mirrored CYP450 inhibitor/substrate reference dataset.
scigantic-cryoet
Search the CZ CryoET Data Portal from Python: a catalog and search layer over ~370 public cryo-electron tomography datasets, none of which the portal itself indexes.
scigantic-transfer
Mirror a Hugging Face dataset into a region-local S3 bucket and load it into memory fast (with HF fallback + benchmark).
