jimmc414
@jimmc414
Public Skills
gtars
by jimmc414
High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.
anndata
by jimmc414
This skill should be used when working with annotated data matrices in Python, particularly for single-cell genomics analysis, managing experimental measurements with metadata, or handling large-scale biological datasets. Use when tasks involve AnnData objects, h5ad files, single-cell RNA-seq data, or integration with scanpy/scverse tools.
fluidsim
by jimmc414
Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water equations, stratified flows, or when analyzing turbulence, vortex dynamics, or geophysical flows. Provides pseudospectral methods with FFT, HPC support, and comprehensive output analysis.
dask
by jimmc414
"Parallel/distributed computing. Scale pandas/NumPy beyond memory, parallel DataFrames/Arrays, multi-file processing, task graphs, for larger-than-RAM datasets and parallel workflows."
fda-database
by jimmc414
"Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research."
chembl-database
by jimmc414
"Query ChEMBL's bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry."
lamindb
by jimmc414
This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spatial, flow cytometry, etc.), tracking computational workflows, curating and validating data with biological ontologies, building data lakehouses, or ensuring data lineage and reproducibility in biological research. Covers data management, annotation, ontologies (genes, cell types, diseases, tissues), schema validation, integrations with workflow managers (Nextflow, Snakemake) and MLOps platforms (W&B, MLflow), and deployment strategies.
gwas-database
by jimmc414
"Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology and polygenic risk scores."
clinvar-database
by jimmc414
"Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine."
bioservices
by jimmc414
"Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO. Unified API for queries, ID mapping, pathway analysis. For direct REST control, use individual database skills (uniprot-database, kegg-database)."
clinicaltrials-database
by jimmc414
"Query ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial details by NCT ID, export data, for clinical research and patient matching."
ena-database
by jimmc414
"Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats."
clinpgx-database
by jimmc414
"Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions."
hmdb-database
by jimmc414
"Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification."
diffdock
by jimmc414
"Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction."
astropy
by jimmc414
Comprehensive Python library for astronomy and astrophysics. This skill should be used when working with astronomical data including celestial coordinates, physical units, FITS files, cosmological calculations, time systems, tables, world coordinate systems (WCS), and astronomical data analysis. Use when tasks involve coordinate transformations, unit conversions, FITS file manipulation, cosmological distance calculations, time scale conversions, or astronomical data processing.
datacommons-client
by jimmc414
Work with Data Commons, a platform providing programmatic access to public statistical data from global sources. Use this skill when working with demographic data, economic indicators, health statistics, environmental data, or any public datasets available through Data Commons. Applicable for querying population statistics, GDP figures, unemployment rates, disease prevalence, geographic entity resolution, and exploring relationships between statistical entities.
geniml
by jimmc414
This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based analysis of genomic regions. Applies to BED file collections, scATAC-seq data, chromatin accessibility datasets, and region-based genomic feature learning.
literature-review
by jimmc414
Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and technical domains. Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles (APA, Nature, Vancouver, etc.).
benchling-integration
by jimmc414
"Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation."
alphafold-database
by jimmc414
"Access AlphaFold's 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology."
datamol
by jimmc414
"Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery: SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly."