"A sandbox environment to run Python code and install dependencies" matching MCP servers:

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).

An MCP server for querying the KEGG bioinformatics database, providing tools, resource templates, and guided prompts for pathways, genes, compounds, and more.

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

Enables analysis of bulk RNA-seq data using natural language queries, executing R and Python in a Docker container with automatic sample anonymization and privacy controls.

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

Enables bioinformatics analysis through natural language conversations with Claude Desktop, automatically generating and executing Python scripts to produce HTML reports and visualizations.

Predicts CRISPR gene dependencies and drug targets by integrating literature, regulatory/PPI networks, and genome-scale metabolic models.

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.

An MCP server for running local LLMs using llama-cpp-python, with built-in tools for generating drug-like molecule SMILES.

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

MCP server that exposes STRING database functionality, allowing AI agents to resolve protein identifiers, retrieve interaction networks, perform homology lookups, and run functional enrichment analysis.

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

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.

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.

Enables protein sequence analysis and structure prediction by extracting ESM-2 embeddings and batch processing FASTA files via Docker. It provides tools for large-scale embedding extraction, job monitoring, and model management within an MCP-compatible environment.

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.

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 server that interfaces with Biomart databases, allowing models to discover biological datasets, explore attributes/filters, retrieve biological data, and translate between different biological identifiers.

A high-performance MCP server that gives LLMs access to 25 biomedical tools federated across 50+ upstream APIs for genes, variants, drugs, diseases, literature, clinical trials, and structural biology.