"Building a solid memory base for AI development" matching MCP servers:

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.

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.

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.

An 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.

An MCP server that provides standardized access to biomedical knowledge bases and resources, enabling AI systems to retrieve verified information from sources like bioRxiv, EuropePMC, and various protein/gene databases.

Allows to retrieve information about an AnnData object via MCP using the read_lazy function from anndata.

Enables running GROMACS molecular dynamics simulations through natural language, with tools for topology building, solvation, simulation management, and trajectory processing via the Model Context Protocol.

Enables 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.

Enables read-only exploration of Copick cryo-ET projects and discovery/validation of copick CLI commands for building processing pipelines.

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

Provides access to UniProt protein sequence and function knowledge base, enabling search and retrieval of protein entries, proteomes, taxonomy, and feature annotations.

Enables AI assistants to explore VEuPathDB WDK catalogs, searches, parameters, and gene data, and to perform gene lookups, expression summaries, step estimates, and download URL retrieval using VEuPathDB credentials.

Provides access to the ClinicalTrials.gov AACT database, enabling analysis of clinical trial data, tracking development trends, and generating therapeutic landscape insights.

Enables LLMs and AI agents to search a biomedical knowledge graph for concepts and study variables, traverse semantic relationships, and look up BioData Catalyst PIC-SURE paths for cohort building.

Framework for building bioengineering automation tools that AI assistants can call via the Model Context Protocol, handling server registration and tool discovery automatically.

Enables querying and retrieving cell line records from the Cellosaurus knowledge base via its REST API, including searching, fetching by accession, and accessing release information.

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.

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.

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