Scanpy MCP is a natural language processing server designed for the single-cell RNA sequencing analysis software Scanpy, supporting operations such as data reading and writing, preprocessing, analysis, and visualization through natural language. It is suitable for researchers and proxy developers.

An unofficial Reactome MCP server that provides a model context protocol service for accessing Reactome pathway and systems biology data. It includes 8 verified functional tools covering bioinformatics analyses such as pathway search, detail acquisition, gene association, and disease mechanism.

PyMOL - MCP is a tool that integrates PyMOL with Claude AI through the Model Context Protocol (MCP), enabling control of molecular visualization and structural analysis through natural language.

This is a Model Context Protocol server for accessing the KEGG biological database. It provides 30 bioinformatics analysis tools, supports HTTP transmission and LangChain integration, and facilitates LLM to call KEGG data for bioinformatics analysis.

ChatSpatial is a natural - language - based MCP server for spatial transcriptomics analysis. It supports more than 60 methods, covering 15 categories such as spatial domain identification, cell communication, and trajectory analysis. It can be used with multiple MCP - compatible AI clients.

An MCP server that provides access to the Protein Data Bank (PDB), supporting functions such as structure search, information retrieval, file download, and quality assessment.

This is a server project that provides Model Context Protocol (MCP) integration for the Galaxy bioinformatics platform, supporting functions such as connecting to Galaxy instances via API, searching and executing tools, managing workflows, managing history records, and uploading files.

The UniProt MCP Server is a service that provides protein information queries, supporting the retrieval of protein function and sequence information through UniProt numbers.

Unofficial STRING database MCP server, providing tools for protein interaction network analysis, functional enrichment and comparative genomics, supporting comprehensive protein network research through the STRING API.

Unofficial MCP server for the STRING database, providing tools for protein interaction network analysis, functional enrichment analysis, and comparative genomics, and supporting access to comprehensive protein data through the STRING API.

An unofficial UniProt MCP server that provides 26 bioinformatics tools, supporting advanced functions such as protein search, structural analysis, and functional annotation, and directly accessing the UniProt database through the REST API.

SCMCP is an MCP server for single-cell RNA sequencing analysis through natural language processing

A UniProt protein information query server based on the Model Context Protocol (MCP), providing services for obtaining protein functions, sequences, and other information. It supports single and batch queries and has caching and error - handling functions.

An unofficial Gene Ontology MCP Server that provides comprehensive access to Gene Ontology (GO) data, supporting AI systems in ontology-based analysis, gene annotation research, and functional enrichment studies.

The AlphaFold MCP Server is a comprehensive platform that provides protein structure prediction analysis tools, supporting functions such as structure retrieval, quality assessment, batch processing, and visualization integration.

The AlphaFold MCP Server provides comprehensive access to the AlphaFold protein structure database, including rich tools such as structure retrieval, confidence analysis, batch processing, and visualization preparation.

This project is an MCP service interface based on the Broad Institute's Liftover tool, providing genome coordinate conversion functions and supporting the conversion of single point, interval, variant, and HGVS formats.

The Bio-OS MCP Server is a tool and prompt server based on the model context protocol, providing workflow management and Docker image building functions for Bio-OS, supporting both local and cloud deployment methods.

Bioconda-MCP-Server is a bioinformatics tool management platform based on Bioconda, providing MCP (possibly referring to a microservice control platform or similar functionality) services.

MCP server for bioinformaticians and computational biologists

OpenGenes-MCP is a server based on the Model Context Protocol (MCP), which provides a standardized interface for the OpenGenes database to access data on aging and longevity research. The server automatically downloads the latest OpenGenes database from the Hugging Face Hub to ensure that users can always access the latest data. The database contains experimental data on lifespan changes, gene classification standards, associations with aging markers, and longevity-related research. It supports converting natural language queries into SQL queries, making it convenient for researchers and AI assistants to use.

The UniProt MCP Server is a service that provides protein information query for language models. It supports searching for proteins, obtaining detailed information, sequences, functional annotations, and structural data from the UniProt database, and can be integrated into AI applications such as Claude Desktop.

An experimental nf-core tools MCP project that provides functions such as pipeline creation and module management

An unofficial GTEx portal MCP server, providing comprehensive access to the gene expression and regulatory data of the GTEx (Genotype - Tissue Expression) project, containing 25 professional tools, supporting gene expression analysis, eQTL association analysis, and genomic data query.

SAMtools MCP provides a standardized operation interface for SAM/BAM/CRAM files, supporting core functions such as format conversion, sorting, and statistics.

The UniProt MCP Server is a service that provides protein information queries. It supports obtaining protein names, functional descriptions, sequences, etc. through UniProt numbers, and also supports batch queries and caching functions.

ChemCP is an MCP application that can render interactive 2D molecular structure diagrams from SMILES strings and calculate and display molecular properties. It is suitable for the fields of medicinal chemistry and bioinformatics.

This project is an MCP server that provides a programmatic interface for the GWAS Catalog REST API, supporting access to GWAS study, variant, trait, and association data and automatically processing large-scale result sets.