"Files" matching MCP servers:

A 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.

Enables 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.

Enables 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.

Enables 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.

A Model Context Protocol (MCP) server that enables AI agent access to Synapse entities such as Datasets, Projects, Folders, Files, Tables, and more.

An interface for the Nipoppy neuroimaging framework that enables AI agents to list files and manage clinical datasets. It facilitates interaction with neuroimaging data organized according to the Brain Imaging Data Structure (BIDS) standard.

Enables AI assistants to generate, validate, and optimize PLUMED input files for molecular dynamics simulations using a set of MCP tools.

Enables AI assistants to generate, validate, and optimize PLUMED input files for molecular dynamics simulations, with templates and performance suggestions.

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

Enables interaction with the RCSB Protein Data Bank to search, analyze, and visualize protein structures. It provides specialized tools for downloading coordinate files and performing structural modifications like residue mutations and metal atom replacements.

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

Enables MCP-compatible AI clients to validate healthcare claims data quality by running completeness, integrity, and temporal checks on CSV files via five callable tools, including profiling and full scans.

Enables protein sequence analysis and structure prediction by extracting ESM-2 embeddings and batch processing FASTA files via Docker. It provides tools for large-scale embedding extraction, job monitoring, and model management within an MCP-compatible environment.