"NetworkX Graph Visualization Tools and Libraries" 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.

Enables LLMs and AI agents to search a biomedical knowledge graph for concepts and study variables, traverse semantic relationships, and look up BioData Catalyst PIC-SURE paths for cohort building.

Enables LLMs and AI agents to query a biomedical knowledge graph stored in RedisGraph, with tools for concept search, synonym enrichment, and study variable discovery through semantic relationships.

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.

MCP server for single-cell lineage tracing analysis, enabling conversational reconstruction, visualization, and heritability analysis of lineage trees using Cassiopeia, pycea, and treedata.

Enables natural language control of UCSF ChimeraX for protein structure visualization, editing, and analysis through MCP clients.

Natural language-driven spatial transcriptomics analysis via MCP. Integrates 60+ methods for preprocessing, visualization, spatial statistics, cell communication, deconvolution, and trajectory analysis.

An MCP server that enables single-cell RNA sequencing analysis through natural language, supporting data processing, visualization, and analysis tasks without requiring coding knowledge.

Agent-callable canine genomics API providing breed-stratified allele frequencies, pathogenicity predictions, and variant-gene-breed-disease knowledge graph for dog DNA.

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 of the Monarch Initiative biomedical knowledge graph for genes, diseases, phenotypes, and their associations through natural language or direct tool calls.

Connects PyMOL to Claude AI through the Model Context Protocol, allowing for conversational structural biology and molecular visualization through natural language commands.

An MCP server that enables scRNA-Seq analysis through natural language, providing tools for data preprocessing, clustering, and biological visualization. It supports both predefined function execution and a flexible code mode powered by a Jupyter backend for automated single-cell transcriptomics workflows.

Integrates GROMACS molecular dynamics simulations with VMD visualization, enabling setup, execution, analysis, and 3D visualization of molecular dynamics workflows through natural language.

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.

A professional MCP server for comprehensive bioinformatics quality control, providing automated FastQC/MultiQC analysis, HTML report parsing, and advanced data visualization for sequencing data.

A unified biomedical graph database that integrates 50+ primary data sources — genes, proteins, compounds, diseases, pathways, and clinical data — into a single queryable graph with billions of cross-reference edges. Its native MCP server gives LLMs direct access to structured, authoritative biomedical data, complementing their reasoning with reliable identifiers and up-to-date database content.

Enables natural language interface for single-cell RNA-Seq analysis using Liana. Supports reading/writing scRNA-Seq data, cell-cell communication analysis, and visualization through circle plots and dotplots.