"Search for free open-source software" matching MCP servers:

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.

Server to search PubMed (PubMed is a free, online database that allows users to search for biomedical and life sciences literature). I have created on a day MCP came out but was on vacation, I saw someone post similar server in your DB, but figured to post mine.

Enables search and retrieval of academic papers from PubMed database with advanced features like MeSH term lookup, publication statistics, and PICO-based evidence search.

Enables 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.

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.

Enables LLM agents to search biomedical literature, retrieve article details, find related papers, manage caching, and download open-access full texts through MCP with structured, agent-friendly responses.

▎ 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.

MCP server for biopharma software infrastructure offering FDA 21 CFR Part 11 audit trails, CDISC SDTM/Allotrope data exports, 4PL dose-response curve fitting, and HIPAA PII/PHI redaction through 10 Zod-validated tools.

BioMCP is an open-source MCP server that connects any AI assistant to 15 open bioinformatics databases with zero configuration. It provides 23 tools for literature, sequences, BLAST, structures, enrichment, annotations, genomes, interactions, variants, domains, compounds, and single-cell data.

An MCP server that connects AI agents to the PEPTOMA open DeSci peptide research platform, enabling peptide sequence analysis, feed search, and peer-review annotations.

Official public, read-only Helena Bioinformatics MCP for source-cited answers about the company and its published products.

Enables AI agents to control RELION 5.x cryo-EM structure determination software through natural language, providing 23 tools for the complete single-particle analysis pipeline.

Federates 13 gene-related MCP backends (gnomAD, GTEx, etc.) behind a single Streamable HTTP endpoint with collision-free namespacing and search-based tool discovery.

Resolve one supported GRCh38 germline variant and return structured, source-backed ACMG/AMP evidence with provenance and explicit limitations. The public server is read-only and intended for professional review.

Enables querying metadata from MyVariant.info, a comprehensive variant annotation database, providing dataset statistics, source information, and build versions.

Enables AI agents to query the WikiPathways open community pathway database via natural language, part of the Pipeworx MCP gateway.

Reproduces the in-silico toxicological profile of Heracleum sosnowskyi metabolites from Rassabina & Fedorov (2025) using open-source models for LD50 prediction, toxicity classification, chemical space clustering, and synthesis cost estimation.

Empowers AI agents with direct access to the official ClinicalTrials.gov database, enabling programmatic searching, retrieval, and analysis of clinical study data through a Model Context Protocol interface.

MCP server and Claude Plugin for a full ENCODE Project genomic data and analysis toolkit — search, download, track, and analyze functional genomics experiments

Enables coding agents to interact with the Reactome pathway database, including search, lookup, hierarchy traversal, SBML/SBGN export, and gene-set enrichment analysis.