"Tools for Creating SWOT Analyses, Competitive Positioning Matrices, and Value Chains" matching MCP servers:

Provides a collection of MCP servers for computational chemistry tasks including molecular generation and retrosynthesis. Also offers property prediction and molecule pricing capabilities.

Parses MS-DIAL binary lipidomics outputs and runs standard analyses server-side, returning compact summaries so an LLM can drive full lipidomics analysis without exposing raw matrices.

Enables deep probabilistic analysis of single-cell omics data using scvi-tools through natural language. Supports SCVI for scRNA-seq analysis, SCANVI for cell type annotation, TOTALVI for multi-modal RNA/protein data, and PEAKVI for scATAC-seq analysis.

A specialized MCP server for Metal-Organic Framework research that provides tools for database searching, structural optimization, and energy calculations via ASE. It enables scientific workflows by allowing users to interact with MOF data and perform chemical simulations through a standard SSE interface.

Enables searching cryo-EM density maps in EMDB and raw datasets in EMPIAR, with filtering by resolution, keyword, and cross-referencing between the two databases.

This server enables multi-agent conversations for interacting with Cirro's biological data platform through its OpenAPI interface, auto-generated using AG2's MCP builder.

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.

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.

Enables Claude Desktop to read and drive analyses on the active MilliMap session, including datasets, clusters, annotations, and markers.

Enables AI clients to connect to Galaxy instances, inspect histories and reports, discover tools and workflows, submit analyses, and monitor their results via interactive cards.

Enables interaction with AnnData objects via the Model Context Protocol, allowing querying and manipulation of annotated data matrices for single-cell genomics.

MCP server for RNA-seq downstream analysis, wrapping R scripts to generate plots and perform analyses like PCA, volcano, heatmap, enrichment, and WGCNA.

Enables natural-language access to R maftools cancer genomics analyses, including mutation summaries, oncoplots, cohort comparisons, mutation signatures, clinical enrichment, survival analyses, and copy-number visualization.

Enables AI clients to access virome datasets and external bioinformatics APIs through MCP tools, including Wikipedia, PubMed, NCBI Taxonomy, read-only SQL over S3 Parquet, pandas/Plotly analyses, and map visualizations, while keeping the client decoupled from data and business logic.

Runs the full HyphAeon report and per-pillar analyses in-process, with MEME concordance, over stdio or streamable HTTP.

An MCP server that grounds protein research in the UniProt SPARQL endpoint, providing tools for querying proteins, sequences, variants, diseases, and more via intent-named tools and raw SPARQL.

Enables language models to search biomedical literature, fetch sequences, and follow links across Entrez databases through eleven read-only tools wrapping the nine NCBI Entrez E-utilities. It handles URL building, pacing, redirects, response caps, and API-key redaction so queries can be answered without a browser or scraping.

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.

Enables AI assistants to clean PDB structures and run initial-stage energy relaxation for biomolecular modeling. It provides a structured workflow for preparing structures before production molecular dynamics or coarse-graining pipelines.

MCP server that provides tools to query harmonized gene-disease validity data from the Gene Curation Coalition, supporting consensus and conflict detection for gene-disease assertions.