Tellurium

COPASI — COmplex PAthway SImulator for systems biology. Simulates and analyzes biochemical reaction networks using deterministic ODE integration (LSODA, Radau5, CVODE), stochastic simulation (Gibson-B

1 shared topic • 2 shared operations

Use when working with BioModels, curated systems biology models, SBML model discovery, model metadata retrieval, model file manifests, COMBINE archive downloads, model identifier validation, or buildi

1 shared topic • 1 shared operation

Use when working with CellNOptR (Cell Network Optimizer in R), a Bioconductor package for training logic-based signaling network models to phosphoproteomic or biochemical data. Covers Prior Knowledge

1 shared topic • 1 shared operation

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,

1 shared topic • 1 shared operation

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

1 shared topic • 1 shared operation