"How to use the terminal or command line interface" matching MCP servers:

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

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.

Provides a programmatic interface to the Genome Aggregation Database (gnomAD) API across versions v2.1.1, v3.1.2, and v4.1.0. It enables users to query gene metadata, variant information, population frequencies, and ClinVar data through a unified schema.

MCP server for querying the GWAS Catalog (EBI/NHGRI), a curated catalog of genome-wide association studies. It enables AI agents to search and retrieve study data via natural language or direct tool calls.

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

Provides a natural language interface for scRNA-Seq analysis using the Scanpy library, supporting operations such as data preprocessing, clustering, and visualization. It enables AI agents and clients to perform complex single-cell transcriptomics workflows through the Model Context Protocol.

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

Enables querying of the Monarch Initiative biomedical knowledge graph for genes, diseases, phenotypes, and their associations through natural language or direct tool calls.

🔍 Enable AI assistants to search, access, and analyze PubMed articles through a simple MCP interface.

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

Enables querying the Human Protein Atlas data using natural language or direct MCP tools, with keyless access via the Pipeworx gateway.

A terminal-based bioinformatics CLI chat tool that integrates Ensembl VEP, NCBI ClinVar, an MCP server layer, and OpenRouter's NVIDIA Nemotron 3 Ultra model to provide variant consequence and clinical significance lookups with clear summaries in a Rich-powered CLI.

Provides a natural language interface for single-cell RNA-Seq analysis using the decoupleR framework. It enables users to perform biological pathway inference, data clustering, and visualization through MCP-compatible AI clients.

Runs the full HyphAeon report and per-pillar analyses in-process, with MEME concordance, over stdio or streamable HTTP.

🔍 Enable AI assistants to search and access bioRxiv papers through a simple MCP interface. The bioRxiv MCP Server provides a bridge between AI assistants and bioRxiv's preprint repository through the Model Context Protocol (MCP). It allows AI models to search for biology preprints and access their

Provides a natural language interface for inferring Copy Number Variations (CNVs) from scRNA-Seq data using the infercnvpy framework. It enables users to perform data preprocessing, CNV inference, and visualization through chromosome heatmaps, UMAP, and t-SNE plots.

A Model Control Protocol implementation for SAMtools, providing a standardized interface for working with SAM/BAM/CRAM files.

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.

An MCP server that grounds protein research in the UniProt SPARQL endpoint, providing tools for querying proteins, sequences, variants, diseases, and more via intent-named tools and raw SPARQL.

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.