"file system" matching MCP servers:

Upload your raw DNA file from 23andMe, AncestryDNA, MyHeritage, FamilyTreeDNA, or any VCF -- and watch a team of AI agents fan out across 16+ public genomics databases, share discoveries with each other in real time, and produce a comprehensive health report. Everything runs on your machine. Nothing is uploaded anywhere.

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.

MCP server for connecting Claude Desktop to a local medical knowledge base with real-time file watching, enabling natural language interaction with medical documents.

Enables searching, retrieving, and downloading protein structure data from the RCSB Protein Data Bank. Supports intelligent protein structure search, comprehensive data retrieval, and multiple file format downloads for bioinformatics research.

MCP server for Kenya health system — NHIF/SHA coverage, facility finder, community health workers, maternal health guidance, essential medicines.

A local-first, model-agnostic MCP server that stores personal health data in a SQLite file and provides analysis-ready views for any AI client to log, retrieve, and reason over health records.

Provides 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.

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.

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

Enables natural language control of quantum photonics experiments through the qudi framework. Supports safe instrument control, measurement execution, and safety system management with built-in runlevel protection and parameter validation.

Enables interaction with a comprehensive healthcare management system through FastAPI, supporting operations for patients, doctors, appointments, medical records, telemedicine, lab orders, prescriptions, insurance claims, and more with JWT authentication.

Enables natural language interaction with the Labguru laboratory management system, providing 63 tools across experiments, protocols, inventory, and more.

Provides secure access to VA's VistA electronic health record system, enabling AI applications to retrieve and summarize patient medical records for clinical staff.

A production-grade MCP server that enables AI assistants to securely manage healthcare data through clinical tools for patient vitals, lab results, and medication ordering. It prioritizes security and compliance with features like HIPAA-ready audit logging, PII redaction, and role-based access control.

Read-only MCP server that lets any LLM query 34 reference APIs of the Japanese ORCA/WebORCA medical billing system, including patients, diseases, medical records, visits, billing, and master data. It is designed for safe, natural-language read access to ORCA data with no write operations.

Enables quantum systems analysis and simulation including quantum circuits, open quantum systems, quantum chemistry calculations, many-body physics, quantum machine learning, and quantum field theory computations.

Connects AI assistants to LabArchives electronic lab notebooks, enabling querying, semantic search, page navigation, and file uploads with provenance tracking.

Enables integration with the Cliniko practice management system through MCP tools and resources. Supports patient management, appointment scheduling, and practice data access through natural language interactions.

Enables AI assistants to query and manage a GxP computerized system inventory as a knowledge graph, including blast-radius impact analysis, regulatory lineage, validation-gap detection, audit-trail-compliant status change approvals, and periodic review generation.

MCP server for the Yari medical system, enabling access to patient records, appointments, financial data, and AI-assisted medical analysis. It provides 18 tools to query and manage medical information through natural language.