One search for your own team's files and the public ecosystem. See how real projects write their agent instructions, and bring the good ideas home.
Files you open will collect here, so you can find them again.
Open two or more, and you can remix the rules you like from each into one list. Kept in this browser only.
garri333Skillgarri333/Skills/skills/11-scientific/clinicaltrials-database/SKILL.md
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.
garri333Skillgarri333/Skills/skills/11-scientific/clinpgx-database/SKILL.md
Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.
garri333Skillgarri333/Skills/skills/11-scientific/clinvar-database/SKILL.md
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.
garri333Skillgarri333/Skills/skills/11-scientific/cobrapy/SKILL.md
Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
garri333Skillgarri333/Skills/skills/11-scientific/cosmic-database/SKILL.md
Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.
garri333Skillgarri333/Skills/skills/11-scientific/dask/SKILL.md
Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clusters. Best for parallel file processing, distributed ML, integration with existing pandas code. For out-of-core analytics on single machine use vaex; for in-memory speed use polars.
garri333Reads credentialsSkillgarri333/Skills/skills/11-scientific/datacommons-client/SKILL.md
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.
garri333Skillgarri333/Skills/skills/11-scientific/datamol/SKILL.md
Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including 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.
garri333Skillgarri333/Skills/skills/11-scientific/deepchem/SKILL.md
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. Best for quick experiments with pre-trained models, diverse molecular representations. For graph-first PyTorch workflows use torchdrug; for benchmark datasets use pytdc.
garri333Skillgarri333/Skills/skills/11-scientific/deeptools/SKILL.md
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
Often used withusfiscaldatasimpytorch-geometric
garri333Reads credentialsSkillgarri333/Skills/skills/11-scientific/denario/SKILL.md
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 research methodologies, executing computational experiments, performing literature searches, or generating publication-ready papers in LaTeX format. Supports end-to-end research pipelines with customizable agent orchestration.
garri333Skillgarri333/Skills/skills/11-scientific/diffdock/SKILL.md
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.
garri333Skillgarri333/Skills/skills/11-scientific/dnanexus-integration/SKILL.md
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
Often used withusfiscaldatasimpytorch-geometric
garri333Skillgarri333/Skills/skills/11-scientific/drugbank-database/SKILL.md
Access and analyze comprehensive drug information from the DrugBank database including drug properties, interactions, targets, pathways, chemical structures, and pharmacology data. This skill should be used when working with pharmaceutical data, drug discovery research, pharmacology studies, drug-drug interaction analysis, target identification, chemical similarity searches, ADMET predictions, or any task requiring detailed drug and drug target information from DrugBank.
garri333Skillgarri333/Skills/skills/11-scientific/ena-database/SKILL.md
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.
Often used withuspto-databasescikit-biostring-database
garri333Skillgarri333/Skills/skills/11-scientific/ensembl-database/SKILL.md
Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.
garri333Skillgarri333/Skills/skills/11-scientific/esm/SKILL.md
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 this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.
garri333Skillgarri333/Skills/skills/11-scientific/etetoolkit/SKILL.md
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
Often used withusfiscaldatascikit-biotorch-geometric
garri333Skillgarri333/Skills/skills/11-scientific/exploratory-data-analysis/SKILL.md
Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generates detailed markdown reports with format-specific analysis, quality metrics, and downstream analysis recommendations. Covers chemistry, bioinformatics, microscopy, spectroscopy, proteomics, metabolomics, and general scientific data formats.
garri333Reads credentialsSkillgarri333/Skills/skills/11-scientific/fda-database/SKILL.md
Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research.
Plain text files in a repository that tell a coding agent how the project works: commands to run, conventions to follow and things to avoid. CLAUDE.md, AGENTS.md, cursor rules and skills are the common kinds.
CLAUDE.md is read by Claude Code. AGENTS.md is an open format that Codex, Cursor and other agents read. Many projects keep one and point the other at it.
A folder with a SKILL.md that describes one capability, such as filling PDFs or reviewing code. The agent loads it only when the task calls for it.
Your agents already can, over MCP, limited to the files you're allowed to read. Searching them from this page is coming.
