Scigantic builds a platform for working with public scientific data: a searchable catalog of thousands of archives, notebooks that mount them directly with no download step, an in-notebook AI assistant with schema-aware context, and fine-tuning pipelines for biological sequence models. scigantic.com
The packages in this org are the query layer underneath that platform, released standalone. Each one is a permissively licensed Python client for a specific public archive or file format, self-contained and usable with no dependency on the rest of Scigantic. Together they're a library of libraries: point-lookups, search, and streaming access over public scientific data, without mirroring a database yourself or downloading more than you need. Using one on its own is a preview of the access layer that Scigantic's contextualized archives and fine-tuning infrastructure are built on top of.
| Package | What it does |
|---|---|
| scigantic-empiar | Stream any of ~3,000 EMPIAR cryo-EM datasets (8.9 PiB) over parallel HTTP range reads, nothing downloaded |
| scigantic-emdb | Search all 60,895 EMDB structures by protein, organism, resolution, molecular weight, or PDB cross-reference |
| scigantic-wwpdb | Fetch any of ~45,000 wwPDB Chemical Component Dictionary ligands and monomers by id, no download |
| scigantic-cryoet | Search ~370 CZ CryoET Data Portal tomography datasets by organism, sample type, disease, or annotation coverage |
| Package | What it does |
|---|---|
| scigantic-chembl | Query ChEMBL directly from a public S3 mirror with DuckDB, no local database |
| scigantic-bindingdb | Query BindingDB the same way, including a live cross-reference bridge into ChEMBL |
| scigantic-pubchem | Live PubChem client with throttle-aware retry, BioAssay/gene/protein/Tox21 coverage, and caching PubChemPy doesn't have |
| scigantic-comptox | Query EPA's ToxCast bioactivity data from a public S3 mirror, plus live Chemical/Hazard/Exposure lookups over EPA's own CCTE API |
| Package | What it does |
|---|---|
| scigantic-headers | Decode scientific file headers (cryo-EM, imaging, flow cytometry, mass spec, sequencing, structural biology) into typed fields. Zero dependencies. |
| scigantic-mcp | MCP server for the Scigantic archive catalog: search thousands of datasets and get LLM-ready schema cards without downloading anything |
pip install scigantic-empiar scigantic-emdb scigantic-wwpdb scigantic-cryoet \
scigantic-chembl scigantic-bindingdb scigantic-pubchem scigantic-comptox \
scigantic-headers scigantic-mcp
Every package here is MIT or MIT-0 licensed, with its own README, tests, and CI. Issues and PRs welcome.
