"Automating the download and deployment of GitHub projects" matching MCP servers:

Enables AI agents to resolve scientific (Latin binomial) names to Open Tree of Life taxon IDs, retrieve full taxonomic details, synonyms, and ancestor lineages, and find the most recent common ancestor of up to 10 taxa within the synthetic tree of life. Runs keylessly over a hosted gateway endpoint or locally via npx.

An MCP server for searching and accessing RNA sequencing datasets from the European Nucleotide Archive (ENA), supporting bulk, single-cell, and spatial transcriptomics with advanced filtering and download capabilities.

Enables LLM agents to search biomedical literature, retrieve article details, find related papers, manage caching, and download open-access full texts through MCP with structured, agent-friendly responses.

MCP server and Claude Plugin for a full ENCODE Project genomic data and analysis toolkit — search, download, track, and analyze functional genomics experiments

An MCP server that gives Claude access to NCBI Datasets v2 — search genome assembly metadata, retrieve taxonomy records, and download data packages without leaving your conversation.

A Model Context Protocol (MCP) server that provides access to the Protein Data Bank (PDB) - the worldwide repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies.

Exposes the NGS360 bioinformatics platform REST API as MCP tools, enabling AI assistants to manage sequencing runs, projects, workflows, and more through natural language.

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

Enables read-only exploration of Copick cryo-ET projects and discovery/validation of copick CLI commands for building processing pipelines.

Enables searching ENA's public sequencing data by organism, study, platform, country or date, retrieving FASTQ/BAM download URLs and checksums, and discovering available result types and fields.

Unified genomic track, peak, and sequence retrieval tool for ENCODE, ChIP-Atlas, ReMap, GEO, and SRA/ENA with unified metadata, resolved DOI/PMID provenance, and direct FASTQ download without SRA toolkit.

Enables interaction with AnnData objects via the Model Context Protocol, allowing querying and manipulation of annotated data matrices for single-cell genomics.

Enables researchers to query DigitalBrain data catalogs, brain region profiles, gene expression summaries, and paper evidence, and download approved results through MCP-compatible clients.

Validates the physical and chemical plausibility of ligand–protein docking poses using the PoseBusters tool.

Enables AI assistants to explore VEuPathDB WDK catalogs, searches, parameters, and gene data, and to perform gene lookups, expression summaries, step estimates, and download URL retrieval using VEuPathDB credentials.

Enables keyless lookup of marine species and genus names, retrieval of full taxonomic lineages by AphiaID, and common vernacular names across languages via MCP tools.

Enables AI agents to query the WikiPathways open community pathway database via natural language, part of the Pipeworx MCP gateway.

Enables querying the EBI Expression Atlas for gene expression data across species and conditions. Part of the Pipeworx gateway, it provides access to baseline and differential expression studies.

Enables querying the CIViC database for clinical interpretations of cancer variants through tools like get_variant_evidence and get_variant_assertions.

Enables AI-powered protein design, including binders, peptides, and custom proteins, with GPU-accelerated Docker deployment and async job management.