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Use when working with iBioSim — a computer-aided design (CAD) tool for modeling, analysis, and synthesis of genetic regulatory networks (GRNs) and synthetic biology circuits. Supports SBML (Systems Bi
Use with AI
Install the MCP server or CLI to instantly fetch iBioSim documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/ibiosim
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
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
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
2 shared topics
pathfindR is an R package for active-subnetwork-oriented pathway enrichment analysis. It maps a gene list (typically a differential expression result with fold-changes and p-values) onto a protein-pro
2 shared topics
Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.
2 shared topics