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maintenanceFramework for building bioengineering automation tools that AI assistants can call via the Model Context Protocol, handling server registration and tool discovery automatically.
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"Using PostgreSQL with n8n Workflow Automation" matching MCP servers:
- AlicenseCqualityBmaintenanceEnables workflow management and Docker image building for Bio-OS platform. Supports WDL workflow submission, validation, and monitoring, along with Docker image building and status tracking for bioinformatics workflows.Last updated225MIT
- Alicense-qualityCmaintenanceMCP server for biological protein design, folding, and affinity prediction using Refua tools, with optional support for ADMET, clinical simulation, preclinical planning, wet-lab automation, and more.Last updatedMIT
- AlicenseAqualityAmaintenancePhylogenetic inference server driving IQ-TREE 2, always returning per-clade bootstrap support plus model selection, tree comparison, and alignment simulation, with detailed diagnostics like conflicting clades and model uncertainty.Last updated5GPL 2.0
- AlicenseAqualityDmaintenanceA Model Context Protocol (MCP) server for interacting with Gen3 data commons, with GraphQL query validation to reduce hallucinations.Last updated54MIT
- FlicenseAqualityCmaintenanceEnables 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.Last updated7
- AlicenseAqualityDmaintenanceA 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.Last updated87MIT
- AlicenseAqualityCmaintenanceAn 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.Last updated111Apache 2.0
- AlicenseAqualityDmaintenanceEnables AI-assisted molecular biology experiment design with tools for qPCR primer design, cloning strategy optimization, TaqMan probe design, and multiplex compatibility analysis.Last updated61MIT
- AlicenseAqualityAmaintenanceAn MCP server that interfaces with Gigwa for genotyping data import, analysis, and audit, enabling users to perform complex workflows through natural language commands.Last updated29Apache 2.0
- AlicenseAqualityFmaintenanceAn 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.Last updated1913817MIT
- AlicenseAqualityAmaintenanceAuditable UniProt MCP server with per-query SHA-256 provenance and offline replayLast updated413Apache 2.0
CEDAR MCP Serverofficial
AlicenseAqualityCmaintenanceEnables interaction with the CEDAR metadata repository, including fetching templates, searching BioPortal ontology terms, and managing template instances.Last updated8MIT- AlicenseAqualityDmaintenanceAn MCP server that provides tools for searching and fetching protein data from the UniProt database using the unipressed library.Last updated2MIT
- AlicenseAqualityCmaintenanceMCP server for single-cell lineage tracing analysis, enabling conversational reconstruction, visualization, and heritability analysis of lineage trees using Cassiopeia, pycea, and treedata.Last updated18MIT
- AlicenseAqualityDmaintenanceEnables AI assistants to query the Ubergraph biomedical ontology SPARQL endpoint with tools for custom SPARQL queries, term lookup, search, and hierarchy traversal.Last updated4MIT
- AlicenseAqualityDmaintenanceConnects 3D Slicer with AI assistants through the Model Context Protocol, enabling medical image processing and scene manipulation using natural language.Last updated338MIT
- AlicenseAqualityDmaintenanceEnables AI-driven pharmacogenomic analysis by querying structured genetic variant, drug response, and disease risk data. Supports natural language questions about medications, traits, and health risks based on user genome data, with privacy-first local execution.Last updated163711MIT
- AlicenseAqualityCmaintenanceConverts messy metabolite names into standard database identifiers (KEGG, HMDB, ChEBI, PubChem, InChIKey) and performs crosswalking to Mouse-GEM for metabolic model input, with deterministic tools and an LLM reasoning layer for identity disambiguation.Last updated20MIT
- AlicenseAqualityAmaintenanceProvides LLMs with structured access to critical biomedical databases including PubTator3 (PubMed/PMC), ClinicalTrials.gov, and MyVariant.info through the Model Context Protocol.Last updated35568MIT
