"Running queries in Apache Superset" matching MCP servers:

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.

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

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

Enables AI assistants to perform genomic variant analysis using OakVar, including running annotation pipelines, managing 200+ annotator modules, querying variant databases, and generating reports in various formats.

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.

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.

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.

Renders interactive 2D molecular structure diagrams from SMILES notation and computes molecular properties like molecular weight, LogP, and TPSA, directly in the chat.

MCP server that provides tools for querying the Human Phenotype Ontology (HPO) including term lookup, hierarchy exploration, cross-ontology mappings, and gene-phenotype-disease associations, all grounded in a local SQLite database for fast offline lookups.

An MCP server that enables AI coding assistants to interact with Rosetta, PyRosetta, and Biotite for running RosettaScripts, validating XML, translating between Rosetta and Biotite, scoring structures, and querying documentation.

▎ Provides 32 tools for plant-genomics locus lookup across 11 free public backends (Ensembl Plants, Phytozome, UniProtKB, Europe PMC, QuickGO, NCBI BLAST, Gramene, KEGG, STRING-DB, ATTED-II, BAR). Takes a TAIR-style locus plus optional organism and returns gene metadata, functional/pathway annotation, interactions, co-expression, and literature — in single-locus, batch, and cross-source synthesis.

Converts natural language queries into Cypher queries against the NASA GeneLab Knowledge Graph, enabling AI-assisted analysis of spaceflight experiments and their biological effects.

Enables AI assistants to query the Ubergraph biomedical ontology SPARQL endpoint with tools for custom SPARQL queries, term lookup, search, and hierarchy traversal.

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

Enables AI agents to conversationally interact with genomics research networks for data analysis and discovery across multiple Omics AI Explorer platforms. It provides tools for exploring data collections, examining table schemas, and executing SQL queries against datasets like Viral AI and Neuroscience AI.

Provides seamless access to the Protein Data Bank in Europe (PDBe) API and search capabilities, enabling AI clients to query protein structures, perform advanced searches, and retrieve structural biology data.

Provides comprehensive access to the UCSC Genome Browser API, enabling queries of genomic data, DNA sequences, gene annotations, variants, and metadata across multiple species and assemblies.

Provides seamless access to UniProtKB protein database, enabling queries for protein entries, sequences, Gene Ontology annotations, full-text search, and ID mapping across 200+ database types.

Intelligent Genomic Data Server Provides high-quality gene information queries, homologous gene analysis, and evolutionary research functions via the MCP protocol.

Enables searching and downloading Gene Expression Omnibus (GEO) data from NCBI, including datasets, series, samples, platforms, and profiles, through natural language queries.