GitHub
rdkit
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows w...
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tools scientific computing AI Skills
Discover tools scientific computing skills, compare source repositories and read the instructions for each workflow.
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deepchem
Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurization options and MoleculeNet benchmarks....
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GitHub
string-database
Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for systems biology.
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GitHub
biomni
Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis. Use this skill when conducting multi-step biomedical rese...
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uniprot-database
Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workflows with multiple databases, prefer bioservices (unified interface to 40+ services). Use thi...
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GitHub
neurokit2
Comprehensive biosignal processing toolkit for analyzing physiological data including ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use this skill when processing cardiovascular signals, brain activity, electr...
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GitHub
fluidsim
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 ana...
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hypothesis-generation
Structured hypothesis formulation from observations. Use when you have experimental observations or data and need to formulate testable hypotheses with predictions, propose mechanisms, and design experiments to...
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GitHub
denario
Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publication. This skill should be used when generating research ideas from datasets, developing re...
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GitHub
biopython
Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioin...
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GitHub
hmdb-database
Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.
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GitHub
cosmic-database
Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.
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GitHub
esm
Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use...
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GitHub
rowan
Cloud-based quantum chemistry platform with Python API. Preferred for computational chemistry workflows including pKa prediction, geometry optimization, conformer searching, molecular property calculations, pro...
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GitHub
clinical-decision-support
Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommenda...
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geo-database
Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.
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GitHub
reactome-database
Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.
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GitHub
alphafold-database
Access AlphaFold 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.
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GitHub
research-lookup
Multi-provider research lookup supporting Gemini Deep Research (60-min comprehensive analysis) and Perplexity Sonar (fast web-grounded research). Intelligently routes between providers based on research mode an...
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GitHub
research-patterns
Research methodology and best practices for finding existing patterns
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GitHub
power-analysis
Calculate statistical power and required sample sizes for research studies. Use when: (1) Designing experiments to determine sample size, (2) Justifying sample size for grant proposals or protocols, (3) Evaluat...
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GitHub
atomic-thought
INVOKE for research tasks and multi-source understanding. Produces visible dependency graphs and contracted answers. Use during research phase of workflow. Triggers: researching topics, gathering information be...
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GitHub
recursion
Recursive algorithms and divide-and-conquer strategies
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GitHub
strings
String algorithms and pattern matching techniques
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The default order uses GitHub repository stars from our indexed data. Stars belong to the source repository and may be shared by multiple skills. They indicate repository interest, not skill installs or an independent quality score.