"Understanding Local File System Operations" matching MCP servers:

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 AI agents to search and retrieve compounds, drugs, diseases, pathways, genes, enzymes, glycans, modules, and KO entries; fetch full parsed flat-file entries by ID; and list database contents through keyless REST tools.

Enables AI agents to resolve marine species names to OBIS taxon records, retrieve georeferenced ocean occurrence records with optional date filtering, and pull aggregate statistics such as record counts, contributing datasets, and observed year ranges. Queries the Ocean Biodiversity Information System keylessly over the Pipeworx gateway or as a local stdio server.

Manages local protein experiments with a Flask backend and SQLite, offering tools for protein library management, Beer-Lambert concentration calculations, BLI dilution planning, and experiment archiving. It provides 7 MCP tools for AI assistants like Claude to interact with the system.

Grounds gene-nomenclature work in the HUGO Gene Nomenclature Committee (HGNC) dataset, enabling resolution of gene symbols and IDs to canonical HGNC identifiers, plus cross-references and batch operations.

MCP server exposing REINVENT4 generative molecular-design operations as validated, LLM-callable tools for drug discovery, including sampling, transfer learning, reinforcement learning, and molecular analysis.

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.

Guides researchers, including those new to BPP, from raw sequence data to a validated control file that has passed a short test run. Wraps BPP command-line tools without running long analyses itself.

MCP server that provides tools for querying the Human Phenotype Ontology (HPO) including term lookup, hierarchy exploration, cross-ontology mappings, and gene-phenotype-disease associations, all grounded in a local SQLite database for fast offline lookups.

Provides local DNA/RNA sequence analysis tools (composition, reverse complement, translation, ORF enumeration, motif scanning) via MCP for agent workflows.

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.

Integrates AlphaFold DB and eight other biomedical data sources into MCP tools for variant clinical reporting, disease-target analysis, structural intelligence, and drug repurposing, with results persisted to a local SQLite knowledge graph.

Provides an MCP interface to the ROBOT command-line tool for OWL ontology editing, enabling operations like merging, reasoning, and conversion via natural language.

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.

An MCP server that lets AI agents record each executed analysis step with SHA-256 hashes of inputs and outputs, validate bioinformatics file formats (FASTA, FASTQ, VCF, BED, GFF/GTF, CSV, TSV, JSON), verify recorded files still match their hashes, replay commands to confirm identical outputs, and generate provenance reports of stored runs.

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.

Enables users to generate volcano plots by submitting jobs with input files and parameters, supporting local or Docker execution.

Enables AI coding agents to search academic papers, resolve biomedical entities, mine relations, and traverse citation graphs using Semantic Scholar and PubTator3, with local caching for reproducibility.

Enables AI assistants to query gene annotations, expression, pathways, variants, and more via the MyGene.info API, supporting batch operations and multiple biological data sources.

Enables users to manage and navigate nf-core bioinformatics pipeline repositories, allowing list, search, and explore operations on pipeline configurations, workflows, and modules.

An MCP server for High-Throughput Screening (HTS) assay calculations across sub-cellular, cellular, tissue, and organism biological tiers, enabling local-first bioassay analysis.

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.

Enables compiling typed decision queries into the smallest decision-sufficient evidence context with machine-checkable Context Certificates, providing auditable executable-biology inference through local MCP tools.

An MCP server that enables AI assistants to generate, score, and analyze DNA sequences using the evo2 genomic foundation model. It supports multiple execution modes including local GPU, SLURM clusters, and the Nvidia NIM cloud API for tasks like variant effect prediction and sequence embedding.

Enables AI agents to search public cancer genomics studies (TCGA, CPTAC, MSK, and more), fetch full details for individual studies, resolve gene symbols to Entrez ids, and list cancer types. Works keylessly against open cBioPortal data over a hosted MCP endpoint, a local stdio server, or plain HTTP.

An MCP server for running local LLMs using llama-cpp-python, with built-in tools for generating drug-like molecule SMILES.

Analyzes a consumer raw DNA file (AncestryDNA, 23andMe, MyHeritage, FTDNA, LivingDNA, VCF) entirely on the user's machine: Y and mtDNA haplogroups, traits, ClinVar scan, PharmCAT pharmacogenomics, and a plain-language report. Tools: analyze, summary, section, lookup, narrative_prompt/set_narrative, clinvar_findings, pharmacogenomics. Nothing is uploaded.

Provides a natural language interface for scRNA-Seq analysis using the Scanpy library, supporting operations such as data preprocessing, clustering, and visualization. It enables AI agents and clients to perform complex single-cell transcriptomics workflows through the Model Context Protocol.

Enables querying roughly 3.2 million measured protein–ligand binding affinities from a local, read-only DuckDB build of the BindingDB MySQL dump, with tools for searching compounds and targets, retrieving potency and selectivity profiles, fetching activity records with assay and citation details, and running read-only SQL.

An MCP server providing public plant bioinformatics APIs including UniProt, NCBI, InterProScan, PDB, AlphaFold, Ensembl Plants, and web-based resources like Sol Genomics and BAR, without local data. It supports gene lookups, protein summaries, structure retrieval, and functional annotations through natural language.