Welcome to pyvipr’s documentation!
pyvipr is an ipython widget for interactively visualizing systems biology models. It uses PySB for generating network data and simulating trajectories and Cytoscape.js to render them. It supports BioNetGen and SBML models through the pysb importer module.
- Installation
- PyViPR Tutorial and PySB interface
- PySB interface
- Import pyvipr pysb_viz module and a PySB model
- Species view
- Communities view
- Bipartite graph with species and bidirectional reactions nodes
- Bipartite graph with species and rules nodes
- Bipartite graph with species and rules nodes from incorrect model
- Bipartite graph with species and rules nodes. Rules are grouped by the functions that were used to create them.
- Bipartite graph with species and rules nodes. Rules are grouped by the modules they come from
- Species graph grouped by the compartment in which they are located
- Using a BioNetGen file (.bngl) to visualize the model
- Visualizing a large rule-based model using the atom-rules graph
- Dynamic visualization of a model
- Tellurium interface
- Other graph formats interface
- PyViPR Core Modules Reference
- PySB static model visualizations (
pyvipr.pysb_viz.static_viz
) - PySB Dynamic model visualizations (
pyvipr.pysb_viz.dynamic_viz
) - PySB visualization views (
pyvipr.pysb_viz.views
) - Tellurium static model visualizations (
pyvipr.tellurium_viz.static_viz
) - Tellurium Dynamic model visualizations (
pyvipr.tellurium_viz.dynamic_viz
) - Tellurium visualization views (
pyvipr.tellurium_viz.views
) - NetworkX static and dynamic visualizations (
pyvipr.networkx_viz.network_viz
) - NetworkX visualization views (
pyvipr.networkx_viz.views
)
- PySB static model visualizations (