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"Managing and Working with Files" matching MCP servers:
CEDAR MCP Serverofficial
AlicenseAqualityAmaintenanceEnables interaction with the CEDAR metadata repository, including fetching templates, searching BioPortal ontology terms, and managing template instances.8MIT- FlicenseAqualityDmaintenanceA TypeScript MCP server for interacting with CDISC Define-XML 2.0 and 2.1 files, enabling users to load, search, and retrieve clinical data metadata including datasets, variables, and codelists. It supports local file processing with document caching and provides responses in both JSON and Markdown formats.13
- FlicenseBqualityDmaintenanceEnables AI agents to query free biomedical and pharmaceutical APIs for clinical trials, drug data, molecular structures, adverse events, and research literature.14
- AlicenseCqualityCmaintenanceEnables AI assistants to query ClinicalTrials.gov and PubMed for research evidence, and to compare regulatory document changes against internal files, with strict read-only access and no ability to modify or export data.5Apache 2.0
- AlicenseCqualityBmaintenanceEnables analysis of FTIR spectra by accepting peak lists, natural-language descriptions, or base64-encoded spectrum files and returning spectral-library candidates from the FTIR.fun API.4MIT
- Alicense-qualityBmaintenanceEnables querying US regulated-care providers (GLP-1 clinics) with tools for searching, retrieving details, and checking compliance, using natural language or function calls.2MIT
- Alicense-qualityFmaintenanceProvides access to Allen Institute for Neural Dynamics (AIND) metadata and data assets through MongoDB queries, aggregation pipelines, NWB file exploration, and AI-powered data summaries.MIT
Bio-MCP FastQC Serverofficial
Alicense-qualityCmaintenanceEnables AI assistants to perform quality control analysis on high-throughput sequencing data using FastQC and MultiQC. It supports single-file and batch processing of FASTQ/FASTA files and generates comprehensive, interactive summary reports.MIT
synapse-mcpofficial
Alicense-qualityAmaintenanceA Model Context Protocol (MCP) server that enables AI agent access to Synapse entities such as Datasets, Projects, Folders, Files, Tables, and more.3MIT
galaxy-mcpofficial
Alicense-qualityAmaintenanceMCP server for interacting with Galaxy bioinformatics platform, enabling AI assistants to connect to Galaxy instances, search and execute tools, manage workflows, and access other features.37MIT- Alicense-qualityDmaintenanceEnables molecular generation, optimization, and analysis through NVIDIA MolMIM API. Supports generating drug-like molecules with desired properties, extracting molecular embeddings, and exploring chemical space around seed molecules.MIT
- Alicense-qualityDmaintenanceEnables interaction with FHIR resources on Google Cloud Healthcare API through a SmartOnFHIR gateway secured by Firebase Auth, providing access to patient data, medical records, and medical research tools like PubMed.1MIT
- Alicense-qualityDmaintenanceEnables MCP clients like Claude Desktop to interact with openEHR REST APIs (EHRbase) for creating compositions, managing EHRs, listing templates, and executing AQL queries.18MIT
- Alicense-qualityCmaintenanceMCP-native scientific skills for reproducible computational biology and AI-driven drug-discovery workflows. It combines deterministic scientific tools with an MCP server to give AI agents real computational capabilities.Apache 2.0
- Alicense-qualityDmaintenanceAn MCP server that provides SNOMED CT clinical terminology lookup via any FHIR R4 terminology server supporting SNOMED CT and ECL. Offers tools for searching by term, fetching by code, and navigating the concept hierarchy.20Apache 2.0
- Alicense-qualityDmaintenanceIntegrates with EMRs like Cerner and Epic via FHIR to retrieve patient data, and provides medical research tools (PubMed, clinical trials, FDA) for clinical analysis.1MIT
- Alicense-qualityAmaintenanceDecodes, searches, validates, and crosswalks US medical codes (ICD-10-CM, ICD-10-PCS, HCPCS Level II) using an offline bundled index via MCP.7862Apache 2.0
- Alicense-qualityAmaintenanceMCP server that exposes STRING database functionality, allowing AI agents to resolve protein identifiers, retrieve interaction networks, perform homology lookups, and run functional enrichment analysis.5MIT
- Alicense-qualityCmaintenanceConnects AI assistants to Nightscout for real-time glucose monitoring, analysis, and treatment logging, enabling natural language interaction with CGM data.4MIT
