"A system for semantically searching local Markdown files" 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).

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

Provides GPU-accelerated scientific computing capabilities including symbolic mathematics, quantum wave mechanics simulations, molecular dynamics, and neural network training through four specialized 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.

A production-ready Model Context Protocol (MCP) server that provides comprehensive access to the BioOntology API for searching, annotating, and exploring over 1,200 biological ontologies.

Enables users to generate volcano plots by submitting jobs with input files and parameters, supporting local or Docker execution.

Enables searching genomic archives and reference databases, retrieving bounded reads, variants, coverage, and sequence data at specific loci from indexed sequencing files, and resolving versioned reference evidence.

Enables searching cancer genes and curated variants from CIViC, retrieving associated diseases, therapies, and graded evidence items and assertions for clinical interpretation.

Connects to NCBI E-utilities for searching, fetching, and linking biological data across Entrez databases.

A specialized MCP server for Metal-Organic Framework research that provides tools for database searching, structural optimization, and energy calculations via ASE. It enables scientific workflows by allowing users to interact with MOF data and perform chemical simulations through a standard SSE interface.

A local-first MCP server that annotates whole-genome VCF files and lets you query pharmacogenomics, disease risk, and carrier status through natural language.

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

Enables searching and retrieving curated mathematical models of biological systems from BioModels, including metadata, source publications, and downloadable model files in SBML, BioPAX, and other formats, with querying by pathway, disease, organism, gene, or author.

Wraps NCBI BLAST+ blastp into a FastMCP service for auditable protein homology searches with local output artifacts and structured metadata.

MCP server for querying BV-BRC biological data, submitting analysis jobs (assembly, annotation, BLAST, etc.), and managing workspace files via natural language.

A Model Control Protocol implementation for SAMtools, providing a standardized interface for working with SAM/BAM/CRAM files.

Enables in-chat scientific viewers for molecular structures, sequence alignments, and slide images, plus data tools for searching structures, fetching sequences, aligning them, and drafting NGS analysis plans.

Manages local protein experiments with a Flask backend and SQLite, offering tools for protein library management, Beer-Lambert concentration calculations, BLI dilution planning, and experiment archiving. It provides 7 MCP tools for AI assistants like Claude to interact with the system.

Enables searching for academic papers and preprints across multiple platforms including Semantic Scholar, arXiv, PubMed, and CrossRef. It provides access to research records, DOI lookups, and journal metadata through a unified interface deployed on Cloudflare Workers.

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.