"A guide to analyzing data effectively" matching MCP servers:

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.

Parses MS-DIAL binary lipidomics outputs and runs standard analyses server-side, returning compact summaries so an LLM can drive full lipidomics analysis without exposing raw matrices.

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).

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

MCP server providing access to the BERtron API for aggregating genomic and environmental data from multiple BER data sources, enabling geospatial search and health checks.

Enables AI assistants to query genetic variant data, gene constraints, and population genetics information from the gnomAD (Genome Aggregation Database) through its GraphQL API. Supports searching for genes and variants, retrieving constraint scores, analyzing population frequencies, and accessing genomic coverage data.

A server that enables AI assistants to interact with cancer genomics data from cBioPortal, allowing users to explore cancer studies, access genomic data, and retrieve mutations and clinical information.

Enables building and analyzing signalling networks from interaction databases through a Model Context Protocol server.

An MCP server that provides access to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, offering 30 tools for searching and analyzing biological data like pathways, genes, and compounds. It supports integration with LangChain and Ollama to enable LLMs to interact with comprehensive genomic and chemical datasets.

A server providing access to NCBI E-utilities API for searching and retrieving data from databases like PubMed, Protein, and Nucleotide.

A unified biomedical graph database that integrates 50+ primary data sources — genes, proteins, compounds, diseases, pathways, and clinical data — into a single queryable graph with billions of cross-reference edges. Its native MCP server gives LLMs direct access to structured, authoritative biomedical data, complementing their reasoning with reliable identifiers and up-to-date database content.

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.

Provides read-only access to the ProPaths verified protein interactome, letting AI agents search proteins, retrieve mechanistic interaction details, and explore pathway ontology through MCP tools, resources, and prompts.

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.