"Files" matching MCP servers:

Enables AI agents to retrieve cited pharmacogenomic and gene-variant information, including drug–gene guidance from CPIC/DPWG and rsID lookups, so responses can quote curated sources instead of relying on memory. A local package also lets users read raw DNA files on their own computer without sending the file data to the remote service.

Enables querying the EMBL-EBI catalog of published polygenic scores through read-only tools that search scores, traits, publications, performance metrics, sample sets, cohorts, and releases, and that trace GWAS studies and resolve ontology and ancestry identifiers. It also lists and downloads the associated scoring-file and metadata files from the catalog's FTP site.

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.

Connects an AI assistant to an InSync Healthcare (Qualifacts) patient portal, letting the signed-in user read their appointments, medications, allergies, messages, forms, surveys, documents, profile and balance, and download portal files. It also sends confirm-gated secure messages, refill and appointment requests, cancellation requests, and uploads an insurance card to their own profile.

Enables AI assistants to query the eggNOG 7 database in natural language for protein lookups, orthologous groups, pairwise orthologs, protein families, taxonomy, and database statistics. Also delivers structured functional annotations such as KEGG KO and GO terms with confidence scores, plus an index of bulk-downloadable data files.

Enables LLM-powered applications to look up bacterial and archaeal taxonomy, search genomes, browse and navigate the taxonomic tree, and compare genomes or find phylogenetic paths between taxa. It works out of the box with a built-in reference dataset covering major phyla and can be pointed at full Genome Taxonomy Database TSV files for comprehensive queries.

Enables users to resolve regulatory entities, query and analyze biological interactions, inspect evidence, export reproducible network data, and download official compressed source files on demand through an online-first, read-only service.

Reads raw lab-instrument files (microscopy, mass spectrometry, chromatography, flow cytometry, NMR, electrophysiology, spectroscopy, plate readers, qPCR) without vendor software, returning metadata, images, spectra and traces as JSON. It also checks files for damage, runs common analyses, and exports to open formats such as OME-TIFF, OME-Zarr, mzML, Parquet and NWB.

Retrieve genomic data from EGA, ENA, ENCODE, GEO and NCBI, read bounded regions from indexed BAM/CRAM, VCF and bigWig files, and query source-attributed reference evidence. Runs locally with 23 MCP tools. MIT-licensed; research use.

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.

Enables AI assistants to search ImmPort immunology studies and subjects, read study data and assay results, look up controlled vocabularies and the data model, and find study files. Supports study comparison, release history lookups, and guided workflows for cross-study analysis.

A local stdio server that lets AI agents search 59 bundled scientific illustration assets, create and edit figure projects through validated, revision-checked operation batches, and export editable SVG, draw.io, or .biocanvas files with attribution. It runs without API keys or remote listeners and confines its writes to named projects inside a configured workspace directory.

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.

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

Enables AI agents to look up what US hospitals charge for a CPT/HCPCS or MS-DRG code near a ZIP — gross charge, discounted self-pay price, and de-identified payer-negotiated rates — sourced from the standard charges files hospitals publish under the CMS price transparency rule. Also compares up to 10 hospitals side by side by CMS Certification Number and reports whether a given hospital's prices are held, and why not, when they aren't.

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 AI assistants to validate CSV exports against schemas, infer schemas from example files, profile datasets, and diff before/after exports for lab/LIMS data-quality checks.

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.

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.

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.

Enables AI agents to build, validate, run, and analyze EEG/BCI pipelines, including uploading EEG data, inspecting datasets and files, running experiment campaigns, and managing live EEG streaming sessions.