MCP directory

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7 MCPs

Showing 7 results on this page

Featured Other
321

breadcrumbsMCP

A Model Context Protocol (MCP) server that discovers and interacts with bioinformatics services through embedded "breadcrumb" metadata in HTML pages.

M Matthias
active
Database Integration
267

UCSCCBmcp

A Model Context Protocol (MCP) server that provides access to UCSC Cell Browser datasets by parsing the dataset.json file from https://cells.ucsc.edu/dataset.json.

M Matthias
active
Database Integration
213

STRING-MCP

A comprehensive Python package for interacting with the STRING database API through a Model Context Protocol (MCP) bridge.

M Matthias
active
Database Integration
205

Gene Expression Omnibus (GEO) MCP

A Model Context Protocol (MCP) server for accessing GEO (Gene Expression Omnibus) data through NCBI E-Utils API. The tool will enable you to search for GEO datasets, series, samples, platforms, and profiles for your LLM. Tested with Claude Desktop, chatGPT has no out of the box support for this tool yet. Claude will automatically use the tools if it fits the context.

M Matthias
active
Database Integration
171

PLSDBmcp

PLSDB MCP Server Model Context Protocol server for interacting with the PLSDB (Plasmid Database) API. This server provides tools to search, filter, and retrieve plasmid data from PLSDB.

M Matthias
active
Clinical Tools
61

Folklore Clinical Variant Interpretation MCP

Official public, read-only MCP from Helena Bioinformatics for clinical germline variant interpretation. It resolves supported GRCh38 SNVs and simple indels, returns source-backed evidence, provenance, automated ACMG/AMP variant-level decision support, and related PubMed literature. It accepts no patient or case context and does not provide a diagnosis or treatment recommendation; qualified genetics professional review is required.

M MCPMed contributor
active
Bioinformatics
44

FlowProof

FlowProof is the execution and provenance layer for MCP-enabled bioinformatics. Where data-access servers (e.g. GEOmcp, STRINGmcp) let an assistant look things up, FlowProof lets it actually run a pipeline and prove the result. Each run emits a Workflow Run RO-Crate recording the pipeline, exact tool versions, parameters, and SHA-256 checksums of every input and output, so an AI-produced result is reproducible byte-for-byte. It runs locally over stdio (your data stays on your machine) or as a hosted HTTP endpoint, and exposes six MCP tools: list, describe, run, status, results, provenance. Seed pipelines: ont-read-stats (Oxford Nanopore read QC, runs on a built-in sample with no input), variant-call-short, rnaseq, fetchngs, viralrecon. Install with: uvx flowproof-mcp

M MCPMed contributor
active