Access Copernicus Climate Data Store (CDS) for ERA5 reanalysis, climate projections, and satellite observations. Use when: (1) retrieving historical weather/climate data, (2) downloading ERA5 reanalysis fields, (3) querying climate projections (CMIP), (4) getting satellite-derived climate variables. NOT for: real-time weather forecasts (use weather APIs), ocean biology (use Copernicus Marine), air quality (use CAMS).
Geospatial and climate data analysis with geopandas and xarray. Use when: (1) geographic vector data analysis, (2) climate and weather NetCDF data, (3) spatial joins and overlay operations, (4) map visualization, (5) CRS transformations and area calculations. NOT for: satellite imagery ML (use rasterio/torchgeo), real-time GPS tracking, or interactive web maps (use folium/leaflet directly).
Query the KEGG REST API for metabolic pathways, genes, compounds, drugs, and diseases. Use when the user needs pathway mapping, gene-to-pathway links, compound info, or cross-reference ID conversion. NOT for protein sequences (use UniProt), 3D structures (use PDB), or variant/SNP data (use NCBI).
Analyzes protein 3D structures, performs homology modeling, interprets AlphaFold predictions, conducts molecular docking, and evaluates protein-ligand interactions; trigger when users ask about PDB files, folding, binding sites, or structural biology.
Query the UniProt REST API for protein sequences, function annotations, structure info, and cross-references. Use when the user needs protein data, gene-to-protein mapping, functional annotation, or FASTA sequences. NOT for nucleotide sequences (use NCBI), 3D structure files (use PDB), or pathway data (use KEGG).
Single-cell RNA-seq analysis with scanpy and anndata. Use when: (1) scRNA-seq preprocessing and QC, (2) clustering and cell type annotation, (3) differential expression analysis, (4) trajectory and pseudotime analysis, (5) UMAP/tSNE visualization. NOT for: bulk RNA-seq differential expression (use DESeq2/edgeR), protein structure analysis (use pdb-structure), or imaging data.
Query the RCSB PDB API for protein 3D structures, experimental metadata, and structure files. Use when the user needs crystal or cryo-EM structure data, PDB entries, resolution info, or structure file downloads. NOT for protein sequences/annotations (use UniProt), gene data (use NCBI), or pathway info (use KEGG).
"Query the Open Targets Platform GraphQL API for gene-drug-disease associations, evidence scores, and therapeutic target validation. Use when the user needs disease associations for a gene, drug evidence for a target, or target prioritization for a disease. NOT for compound property lookup (use pubchem-compound), NOT for bioactivity measurements (use chembl-drug), NOT for protein 3D structures (use pdb-structure)."
Query NCBI E-utilities for GenBank sequences, gene info, SNPs, ClinVar variants, and literature links. Use when the user needs nucleotide/protein sequences from GenBank, gene summaries, variant data, or cross-database links. NOT for protein annotations (use UniProt), 3D structures (use PDB), or pathway mapping (use KEGG).
Orchestrates a genomics analysis workflow from gene query through expression analysis to pathway enrichment. Use when investigating gene function, analyzing expression data, or performing pathway-level interpretation. NOT for pure protein structure modeling or drug-target interaction analysis.
Performs genomics analyses including gene expression profiling, BLAST sequence alignment, GWAS interpretation, variant calling, and genome assembly tasks; trigger when the user mentions DNA/RNA sequences, SNPs, gene panels, or comparative genomics.
"Bioinformatics operations via Biopython. Use when: user asks about DNA/protein sequences, BLAST, or PDB structures. NOT for: clinical genomics or variant calling pipelines."
Performs bioinformatics analyses including pathway enrichment, gene ontology analysis, protein-protein interaction networks, multi-omics integration, and biological sequence database querying; trigger when users discuss gene sets, biological pathways, functional annotation, or omics data integration.
Orchestrates a full drug discovery workflow from target identification through lead optimization. Use when searching for drug candidates against a biological target, evaluating compound libraries, or optimizing hits for drug-likeness. NOT for pure protein structure analysis or single-compound lookups.
"Query the ChEMBL REST API for drug-target interactions, bioactivity data, ADMET properties, and approved drug information. Use when the user needs drug mechanism of action, binding affinity data, target information, or pharmacokinetic properties. NOT for basic compound lookup (use pubchem-compound), NOT for gene-disease associations (use open-targets), NOT for protein 3D structures (use pdb-structure)."
Supports drug discovery workflows including target identification, virtual screening, ADMET prediction, lead optimization, pharmacokinetics modeling, and drug repurposing analyses; trigger when users discuss drug targets, compound libraries, medicinal chemistry, or pharmaceutical development.
Computational chemistry tools including molecular structure, chemical reactions, thermodynamics, spectroscopy analysis, and cheminformatics. Use when user works with chemical formulas, molecular structures, reaction balancing, thermodynamic calculations, or chemical databases (PubChem, ChemSpider). Triggers on "chemical structure", "molecular weight", "balance equation", "reaction", "thermodynamics", "spectroscopy", "SMILES", "PubChem", "chemical formula", "stoichiometry".
Physics problem solving including classical mechanics, electromagnetism, thermodynamics, quantum mechanics, optics, and computational physics. Use when user asks to solve physics problems, simulate physical systems, derive equations, or do unit conversions. Triggers on "physics problem", "Newton's law", "electromagnetic", "quantum", "thermodynamics", "optics", "wave equation", "Schrödinger", "relativity", "unit conversion", "circuit analysis".
Query the Materials Project API v3 for crystal structures, band gaps, formation energies, and thermodynamic stability of 150k+ inorganic materials. Use when: (1) searching materials by chemical formula, (2) looking up material properties by MP ID, (3) filtering materials by band gap, energy, or density, (4) finding stable phases for a composition. NOT for: organic molecules (use pubchem-compound), proteins (use uniprot-protein), drug compounds (use chembl-drug).
Design rigorous scientific experiments with power analysis and controls. Use when: user needs to plan an experiment, calculate sample sizes, or set up controls. NOT for: running experiments or analyzing collected data.
Scientific programming best practices including reproducible research, computational notebooks, version control for research, data management, HPC/parallel computing, and research software engineering. Use when user needs help with research code organization, reproducibility, scientific Python/R workflows, or computational infrastructure. Triggers on "reproducible research", "research code", "scientific computing", "HPC", "parallel computing", "Jupyter", "notebook", "data management plan", "research software", "code review for science".
Verify scientific claims, check calculations, validate experimental designs, and fact-check citations. Use when: (1) checking a claim against evidence, (2) validating statistical analyses, (3) verifying experimental reproducibility claims, (4) fact-checking references, (5) adversarial review of research. NOT for: generating new content (use scienceclaw-generation), simple QA (use scienceclaw-qa).
# Reproducibility Checklist — Open Science Best Practices
