"Agent File Control MCP Server" 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 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.

Enables compiling typed decision queries into the smallest decision-sufficient evidence context with machine-checkable Context Certificates, providing auditable executable-biology inference through local MCP tools.

Enables AI agents to search and retrieve compounds, drugs, diseases, pathways, genes, enzymes, glycans, modules, and KO entries; fetch full parsed flat-file entries by ID; and list database contents through keyless REST tools.

Enables AI agents to read and manipulate networks, tables, visual styles, and more in a live Cytoscape Web session through natural language, by connecting over Chrome DevTools Protocol.

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

Enables prediction of blood-brain barrier permeability for drug molecules via machine learning, with molecule name lookup, plain-language explanations, similar drug search, and applicability domain checks. Exposes these as MCP tools and orchestrates them via a LangGraph agent.

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.

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.

Provides local DNA/RNA sequence analysis tools (composition, reverse complement, translation, ORF enumeration, motif scanning) via MCP for agent workflows.

Enables querying the EMBL-EBI catalog of published polygenic scores through read-only tools that search scores, traits, publications, performance metrics, sample sets, cohorts, and releases, and that trace GWAS studies and resolve ontology and ancestry identifiers. It also lists and downloads the associated scoring-file and metadata files from the catalog's FTP site.

An MCP server that lets AI agents record each executed analysis step with SHA-256 hashes of inputs and outputs, validate bioinformatics file formats (FASTA, FASTQ, VCF, BED, GFF/GTF, CSV, TSV, JSON), verify recorded files still match their hashes, replay commands to confirm identical outputs, and generate provenance reports of stored runs.

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.

Enables natural language control of UCSF ChimeraX for protein structure visualization, editing, and analysis through MCP clients.

Enables searching, retrieving, and downloading protein structure data from the RCSB Protein Data Bank. Supports intelligent protein structure search, comprehensive data retrieval, and multiple file format downloads for bioinformatics research.

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

Agent-callable canine genomics API providing breed-stratified allele frequencies, pathogenicity predictions, and variant-gene-breed-disease knowledge graph for dog DNA.

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.

A collaborative BrAPI v2.1 workspace for multi-agent research via MCP, enabling search and retrieval of studies, germplasm, genotypes, and more across any BrAPI v2-compliant server.

Enables installing, configuring, and running modular MCP servers for biology, bioinformatics, and bioimaging tasks, including local image analysis, ImageJ/Fiji bridging, and LLM-based agent workflows.

Unified MCP server providing AI-agent-ready access to AlphaFold, PubMed, ChEMBL, Ensembl, and 37+ scientific databases.

A professional MCP server for comprehensive bioinformatics quality control, providing automated FastQC/MultiQC analysis, HTML report parsing, and advanced data visualization for sequencing data.

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.

A self-driving cheminformatics MCP server that dynamically exposes a growing library of RDKit-based molecular analysis tools (fingerprints, descriptors, substructure matching, drug-likeness filters, and more) as MCP tools, with each skill autonomously implemented and tested by an agent loop without human intervention.

Enables Claude Code to interact with a TACC or SLURM HPC cluster for bioinformatics pipelines, allowing job management, log reading, file browsing, remote script execution, and job submission through natural language.

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

This server enables multi-agent conversations for interacting with Cirro's biological data platform through its OpenAPI interface, auto-generated using AG2's MCP builder.