COPASI

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

2 shared topics • 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,

2 shared topics • 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

2 shared topics • 1 shared operation

PySB is a Python framework for rule-based mathematical modeling of biochemical systems. Use this skill for mechanistic signaling models, reaction-rule model construction, deterministic or stochastic s

2 shared topics • 1 shared operation

Use when working with ReactomeFIViz — a Cytoscape 3 app for Reactome Functional Interaction (FI) network analysis. Visualizes and analyzes the Reactome FI network (~300k functional interactions among

2 shared topics • 1 shared operation