jimmc414/kosmos

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uspto-database Access USPTO APIs for patent/trademark searches, examination history (PEDS), assignments, citations, office actions, …

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alphafold-database Access AlphaFold's 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files…

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anndata This skill should be used when working with annotated data matrices in Python, particularly for single-cell genomics …

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arboreto Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use wh…

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astropy Comprehensive Python library for astronomy and astrophysics. This skill should be used when working with astronomical…

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benchling-integration Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build…

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biomni Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecu…

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biopython Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence m…

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biorxiv-database Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints…

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chembl-database Query ChEMBL's bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioact…

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clinicaltrials-database Query ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial det…

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clinpgx-database Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele f…

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clinvar-database Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classification…

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cobrapy Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biolog…

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cosmic-database Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusi…

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dask Parallel/distributed computing. Scale pandas/NumPy beyond memory, parallel DataFrames/Arrays, multi-file processing, …

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datacommons-client Work with Data Commons, a platform providing programmatic access to public statistical data from global sources. Use …

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datamol Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery:…

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deepchem Molecular machine learning toolkit. Property prediction (ADMET, toxicity), GNNs (GCN, MPNN), MoleculeNet benchmarks, …

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deeptools NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), …

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denario Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publi…

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diffdock Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual s…

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dnanexus-integration DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, …

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drugbank-database Access and analyze comprehensive drug information from the DrugBank database including drug properties, interactions,…

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ena-database Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by a…

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etetoolkit Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NC…

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flowio Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert t…

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gene-database Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenot…

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geniml This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for tra…

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geo-database Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), r…

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get-available-resources This skill should be used at the start of any computationally intensive scientific task to detect and report availabl…

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gget CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases: gen…

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gtars High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic re…

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gwas-database Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-va…

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hmdb-database Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biom…

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hypogenic Automated hypothesis generation and testing using large language models. Use this skill when generating scientific hy…

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labarchive-integration Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate wi…

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lamindb This skill should be used when working with LaminDB, an open-source data framework for biology that makes data querya…

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latchbio-integration Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serve…

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medchem Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexit…

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metabolomics-workbench-database Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data,…

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molfeat Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert S…

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networkx Comprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python. Use when workin…

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openalex-database Query and analyze scholarly literature using the OpenAlex database. This skill should be used when searching for acad…

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opentargets-database Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetic…

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pathml Computational pathology toolkit for analyzing whole-slide images (WSI) and multiparametric imaging data. Use this ski…

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pdb-database Access RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/…

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pdf PDF manipulation toolkit. Extract text/tables, create PDFs, merge/split, fill forms, for programmatic document proces…

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polars Fast DataFrame library (Apache Arrow). Select, filter, group_by, joins, lazy evaluation, CSV/Parquet I/O, expression …

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protocolsio-integration Integration with protocols.io API for managing scientific protocols. This skill should be used when working with prot…

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