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Use when working with NetworkX, graph analysis in Python, biological network analysis, protein-protein interaction networks, gene regulatory networks, metabolic networks, pathway analysis, network top
Use with AI
Install the MCP server or CLI to instantly fetch NetworkX documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/networkx
Use when visualizing, analyzing, or manipulating biological networks with Cytoscape, the industry-standard desktop platform for systems biology and pathway analysis. Covers network import (SIF, XGMML,
2 shared topics • 2 shared operations
Cytoscape.js — JavaScript graph theory library for network visualization and analysis in the browser and Node.js. Renders interactive biological networks, protein-protein interaction graphs, pathway d
2 shared topics • 2 shared operations
BioGRID — curated repository of protein-protein interactions, genetic interactions, chemical interactions, and post-translational modifications from the published literature. Provides REST API (v4+) f
2 shared topics • 1 shared operation
COPASI — COmplex PAthway SImulator for systems biology. Simulates and analyzes biochemical reaction networks using deterministic ODE integration (LSODA, Radau5, CVODE), stochastic simulation (Gibson-B
2 shared topics • 1 shared operation
ProDy — Python library for protein dynamics analysis and structural bioinformatics. Provides elastic network models (GNM, ANM), principal component analysis (PCA) of structural ensembles and MD trajec
2 shared topics • 1 shared operation