Python Scientific Commons

python-scientific-commons

Atlas of scientific-Python skills, grouped by domain. Each domain's canonical entry sits at the top; the rest are siblings reachable by name.

Cheminformatics / drug discovery

rdkit · datamol · medchem · molfeat · chembl-database · drugbank-database · pubchem-database · zinc-database · pytdc · diffdock · deepchem

Primary entry: rdkit. Modern wrappers: datamol · medchem. Featurization: molfeat. Datasets: pytdc. Docking: diffdock. Catalog DBs: chembl-database · drugbank-database · pubchem-database · zinc-database.

Omics / single-cell / genomics

scanpy · anndata · lamindb · cellxgene-census · pydeseq2 · scvi-tools · scikit-bio · biopython · bioservices · gget · geniml · gtars · gene-database · geo-database · ensembl-database · clinvar-database · clinpgx-database · gwas-database · string-database · reactome-database · kegg-database · opentargets-database

Primary entry: scanpy. Anndata core: anndata · lamindb. Tooling: scvi-tools · pydeseq2. Genomic intervals: geniml · gtars. Sequences/proteins: biopython · bioservices · gget · scikit-bio. Reference DBs: the *-database family above.

Mass-spec / metabolomics

pyopenms · matchms · metabolomics-workbench-database · hmdb-database · brenda-database

Primary entry: pyopenms. Spectral matching: matchms. Reference: metabolomics-workbench-database · hmdb-database · brenda-database.

Medical imaging / clinical

pydicom · pathml · histolab · pyhealth · clinical-decision-support · clinical-reports · clinicaltrials-database · fda-database

Primary entry: pydicom. Histology: pathml · histolab. EHR + reports: pyhealth · clinical-decision-support · clinical-reports. Clinical reference: clinicaltrials-database · fda-database.

Structural biology / proteins / PDB

alphafold-database · pdb-database · uniprot-database · vertex-ai-protein-interleave · vertex-protein-bisimulation · adaptyv

Primary entry: alphafold-database. Structure refs: pdb-database · uniprot-database. Inference pipelines: vertex-ai-protein-interleave · vertex-protein-bisimulation · adaptyv.

Lab automation / experimental

opentrons-integration · pylabrobot · benchling-integration · protocolsio-integration · dnanexus-integration · omero-integration · latchbio-integration · labarchive-integration

Primary entry: pylabrobot. Cloud-lab: latchbio-integration · dnanexus-integration. Imaging stores: omero-integration.

Neuroscience

neuropixels-analysis · etetoolkit · neurokit2 · comrade-vlbi

Primary entry: neuropixels-analysis. Phylogenetic trees: etetoolkit. Physiological signal proc: neurokit2.

PDE / dynamics / sim

fluidsim · simpy · flowio · langevin-dynamics · geomstats-fisher-rao · pymoo · astropy

Primary entry: fluidsim. Discrete event: simpy. Cytometry-style flow data: flowio. Stochastic dynamics: langevin-dynamics. Manifold geometry: geomstats-fisher-rao. Multi-objective: pymoo.

ML / RL / optimization

pytorch-lightning · transformers · vllm-deployment · torch_geometric · pufferlib · stable-baselines3 · gym · gflownet · jaxlife-open-ended · multidispatch-rl · umap-learn · vaex · dask · polars · seaborn · matplotlib · plotly · scikit-learn · scikit-survival · statsmodels · pymc

Primary entry: pytorch-lightning. LLM serving: vllm-deployment · transformers. Graph NN: torch_geometric. RL: pufferlib · stable-baselines3 · gym · gflownet. ML-on-large-data: dask · vaex · polars. Embedding viz: umap-learn. Bayes: pymc. Stats: statsmodels · scikit-learn · scikit-survival. Plotting: seaborn · matplotlib · plotly.

Quantum

qutip · qiskit · cirq · pennylane

Primary entry: qiskit. Open-system: qutip. Variational: pennylane · cirq.

Cross-family threading

• omics → ML: anndata ↔ scvi-tools ↔ pytorch-lightning (probabilistic single-cell models)
• chem → ML: rdkit ↔ molfeat ↔ torch_geometric (graph molecule featurization)
• structures → AI: alphafold-database ↔ vertex-ai-protein-interleave ↔ adaptyv
• dynamics → categorical: langevin-dynamics ↔ geomstats-fisher-rao ↔ koopman-generator (Para(Optic) ▷ Play layer)
• databases → DuckDB: any *-database skill loads cleanly via duckdb-guard + read_csv for tabular reference data

yb-translator parable

CONCEPT: scientific-Python tooling stack
BIOLOGY: cellular metabolic network with substrate-channeling enzyme complexes
ONTOLOGY: GO — metabolic process (GO:0008152), catalytic activity (GO:0003824),
          protein-containing complex (GO:0032991)
EXAMPLE: rdkit (input substrate processing) ⇒ molfeat (featurization, like ATP-coupling)
         ⇒ torch_geometric (transformation enzyme) ⇒ scvi-tools (model fitting,
         downstream regulation). Each tool is one enzyme; the pipeline is the network.

Use when

• Picking the right scientific-Python library for a task
• Threading data across cheminformatics/omics/imaging substrates
• Locating an EBI/UniProt/Ensembl reference DB client
• Wrapping a Python pipeline as a Para(Optic) atom with langevin-dynamics-style forward + Bayesian backward

Atlas family

• REPL substrate: repl-commons
• Categorical substrate: para-mensch-commons
• Protocol substrate: acp-commons
• Scientific-Python substrate: this skill