"Guidance on Writing Software" matching MCP servers:

Enables AI agents to control RELION 5.x cryo-EM structure determination software through natural language, providing 23 tools for the complete single-particle analysis pipeline.

Enables natural language interface for single-cell RNA-Seq analysis using Liana. Supports reading/writing scRNA-Seq data, cell-cell communication analysis, and visualization through circle plots and dotplots.

Enables AI-driven pharmacogenomic analysis by querying structured genetic variant, drug response, and disease risk data. Supports natural language questions about medications, traits, and health risks based on user genome data, with privacy-first local execution.

Enables Claude Desktop to read and drive analyses on the active MilliMap session, including datasets, clusters, annotations, and markers.

MCP server for biopharma software infrastructure offering FDA 21 CFR Part 11 audit trails, CDISC SDTM/Allotrope data exports, 4PL dose-response curve fitting, and HIPAA PII/PHI redaction through 10 Zod-validated tools.

Server to search PubMed (PubMed is a free, online database that allows users to search for biomedical and life sciences literature). I have created on a day MCP came out but was on vacation, I saw someone post similar server in your DB, but figured to post mine.

Enables workflow management and Docker image building for Bio-OS platform. Supports WDL workflow submission, validation, and monitoring, along with Docker image building and status tracking for bioinformatics workflows.

Enables users to manage and navigate nf-core bioinformatics pipeline repositories, allowing list, search, and explore operations on pipeline configurations, workflows, and modules.

Enables AI assistants to perform quality control analysis on high-throughput sequencing data using FastQC and MultiQC. It supports single-file and batch processing of FASTQ/FASTA files and generates comprehensive, interactive summary reports.

Annotate variants by with a deep and rich set of data. Can annotate: genetic change, rsID, CAid, HGVS (g./c./p.), protein change.

An MCP server that provides access to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, offering 30 tools for searching and analyzing biological data like pathways, genes, and compounds. It supports integration with LangChain and Ollama to enable LLMs to interact with comprehensive genomic and chemical datasets.

Enables reproducible target-disease evidence dossier assembly and validation by replaying frozen Open Targets GraphQL responses and checking citations and structured assertions against deterministic scientific contracts.

🔍 A biomedical literature annotation and relationship mining server based on PubTator3, providing convenient access through the MCP interface.

Enables on-demand querying of live NASA POWER weather anomalies and NCBI Pathogen Detection genomic antimicrobial-resistance data for causal analysis.

Enables searching for academic papers and preprints across multiple platforms including Semantic Scholar, arXiv, PubMed, and CrossRef. It provides access to research records, DOI lookups, and journal metadata through a unified interface deployed on Cloudflare Workers.