"How to run desktop commands on a computer" matching MCP servers:

An embedded MCP server for Cytoscape Desktop that lets AI agents load networks, set active views, and control the desktop application over HTTP.

Enables genomic sequence analysis through the Evo 2 model, supporting DNA sequence scoring, embedding, generation, and variant effect prediction with multiple model checkpoints (7B, 40B, 1B parameters).

Enables variant annotation and effect prediction using the Ensembl VEP API, with support for batch and single queries.

Enables AI agents to retrieve cited pharmacogenomic and gene-variant information, including drug–gene guidance from CPIC/DPWG and rsID lookups, so responses can quote curated sources instead of relying on memory. A local package also lets users read raw DNA files on their own computer without sending the file data to the remote service.

Guides researchers, including those new to BPP, from raw sequence data to a validated control file that has passed a short test run. Wraps BPP command-line tools without running long analyses itself.

Enables AI assistants to run reproducible bioinformatics pipelines over MCP, with verifiable provenance via checksums and Workflow Run RO-Crate metadata.

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

Run real bioinformatics from your AI agent on your own GPUs: MMseqs2 homology search, ESMFold structure prediction and sequence tools for Claude, Cursor and Codex. GPU-aware scheduling for shared machines, fail-fast input checks, background jobs, agent-friendly results and provenance for every run.

A framework that integrates Brain-Computer Interface technology with the Model Context Protocol to enable real-time neural signal processing and AI-powered interactions for healthcare, accessibility, and research applications.

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 AI agents to search, filter, download files, and generate reports from the IGVF Data Portal using natural language commands.

Bridge any AI coding assistant directly to GenePattern — run bioinformatics modules, manage cloud jobs, and stream results, all through natural language.

Enables searching a manually curated database of stable macromolecular protein complexes by protein or complex name, gene, GO term, or biological process, and fetching individual records by accession to retrieve subunits with UniProt identifiers, biological roles, and stoichiometry. Complements UniProt, IntAct, and STRING, and can be used keyless over a hosted gateway endpoint or run locally over stdio.

Exposes pipen bioinformatics pipelines as MCP tools, allowing AI assistants to discover and run complex workflows through a progressive disclosure interface.

Enables LLM agents to design proteins, predict structures, score interfaces, and run molecular dynamics simulations through a unified interface.

Enables Claude, Cursor, or any MCP client to query public Drosophila connectome datasets and run in-silico experiments on them locally, with every answer carrying built-in controls, uncertainty, and provenance. Currently exposes dataset listing with licence, citation, download size, and locally cached level details.

Connects PyMOL to Claude AI through the Model Context Protocol, allowing for conversational structural biology and molecular visualization through natural language commands.

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

Enables AI assistants to query VirtualFlyBrain data, run queries, and search for terms related to Drosophila neurobiology.

A Model Context Protocol server that enables AI assistants to interact with LAMMPS for molecular dynamics simulations through natural language commands.

Enables AI assistants to query VCF files through MCP tools that summarize variants, identify pathogenic and carrier variants, interpret pharmacogenomic results, and determine APOE status, with web app and Claude Desktop support.

BioOpenMCP enables users to run bioinformatics tools like FastQC, Cutadapt, and STAR with background execution and status checking. It integrates with Claude Desktop to perform quality control, trimming, alignment, and reporting via natural language.

Control PyMOL from Cursor via natural language. Enables describing molecular structures and styles in plain language to execute PyMOL commands through XML-RPC.

Enables language models to search biomedical literature, fetch sequences, and follow links across Entrez databases through eleven read-only tools wrapping the nine NCBI Entrez E-utilities. It handles URL building, pacing, redirects, response caps, and API-key redaction so queries can be answered without a browser or scraping.

Grounds gene-nomenclature work in the HUGO Gene Nomenclature Committee (HGNC) dataset, enabling resolution of gene symbols and IDs to canonical HGNC identifiers, plus cross-references and batch operations.

Enables AI assistants to clean PDB structures and run initial-stage energy relaxation for biomolecular modeling. It provides a structured workflow for preparing structures before production molecular dynamics or coarse-graining pipelines.

MCP server that provides tools to query harmonized gene-disease validity data from the Gene Curation Coalition, supporting consensus and conflict detection for gene-disease assertions.

Enables coding agents to interact with the Reactome pathway database, including search, lookup, hierarchy traversal, SBML/SBGN export, and gene-set enrichment analysis.

Provides direct SQL access to a locally hosted Reactome database, enabling schema discovery, guarded read-only queries, and ergonomic helpers over the full relational schema.

A Model Context Protocol (MCP) server for interacting with Gen3 data commons, with GraphQL query validation to reduce hallucinations.