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bioRxiv · 10.64898/2026.09.03.749120

Democratizing Agentic Access to Bioinformatics and Biopharmaceutical Databases and Analyses with BioMCP-TS

Yuan, Y.
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Abstract

Practitioners want to give AI agents direct access to biomedical databases and analyses, but today that means choosing between dependency-heavy skill packages, data-lookup-focused server tools, and closed vendor platforms. BioMCP-TS removes the choice: one open-source server that installs with a single pinned command and verifies its own setup. An agent working through BioMCP-TS can search and cross-reference 50+ bioinformatics, pharmaceutical, and patent databases (genes, variants, drugs, diseases, literature, clinical trials, patents, functional genomics, and structures) and, uniquely among open bioinformatics servers, run heavyweight analyses in-process as WebAssembly: Bioconductor differential expression and htslib genomics operations with no R installation, C toolchain, or containers on the host, plus read-only SQL over curated local databases. We demonstrate these strengths with seven practical cases spanning drug-target due diligence, translational intelligence, GWAS follow-up, dependency analysis, cohort genomics, and differential expression, ranging from a first federated lookup through target-disease landscapes to published-structure shortlists and reproducible RNA-seq results, each answered end-to-end within minutes. The server, recorded transcripts, and the full problem set are available at https://github.com/yeyuan98/biomcp-ts (npm: biomcp).

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Yuan, Y.. 2026-09-08. Democratizing Agentic Access to Bioinformatics and Biopharmaceutical Databases and Analyses with BioMCP-TS. https://doi.org/10.64898/2026.09.03.749120

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