Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL,...
AI & LLM
LLM integrations, prompt engineering, and AI orchestration
7,400 skills
Query CZ CELLxGENE Census (61M+ cells). Filter by cell type/tissue/disease, retrieve expression data, integrate with...
Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems...
Parallel/distributed computing. Scale pandas/NumPy beyond memory, parallel DataFrames/Arrays, multi-file processing,...
Work with Data Commons, a platform providing programmatic access to public statistical data from global sources. Use...
Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug...
Molecular machine learning toolkit. Property prediction (ADMET, toxicity), GNNs (GCN, MPNN), MoleculeNet benchmarks,...
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks),...
Multiagent AI system for scientific research assistance that automates research workflows from data analysis to...
Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual...
Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across...
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy,...
Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert...
This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for...
CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases:...
High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic...
Digital pathology image processing toolkit for whole slide images (WSI). Use this skill when working with...
Automated hypothesis generation and testing using large language models. Use this skill when generating scientific...
This skill should be used when working with LaminDB, an open-source data framework for biology that makes data...
Convert various file formats (PDF, Office documents, images, audio, web content, structured data) to Markdown...
Mass spectrometry analysis. Process mzML/MGF/MSP, spectral similarity (cosine, modified cosine), metadata...
Foundational plotting library. Create line plots, scatter, bar, histograms, heatmaps, 3D, subplots, export...
Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts,...
Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert...