"How to run local command-line commands" matching MCP servers:

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.

Provides an MCP interface to the ROBOT command-line tool for OWL ontology editing, enabling operations like merging, reasoning, and conversion via natural language.

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.

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.

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

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.

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 querying and retrieving cell line records from the Cellosaurus knowledge base via its REST API, including searching, fetching by accession, and accessing release information.

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.