PySB Modules Reference

• PySB core (pysb.core)
• ODE integrators (pysb.integrate)
• Simulation tools (pysb.simulator)
• Set/get paths for external tools (pysb.pathfinder)
• Testing PySB Models (pysb.testing.modeltests)
• BioNetGen integration (pysb.bng)
• Kappa integration (pysb.kappa)
• Macros (pysb.macros)
• Pattern matching against PySB models (pysb.pattern)
• Visualizing model structure
  • Render a model’s reaction network (pysb.tools.render_reactions)
    • Usage
    • Output for Robertson example model
  • Render a model’s species (pysb.tools.render_species)
• Sensitivity anaylsis (pysb.tools.sensitivity_analysis)
• Importing from other formats (pysb.importers)
• Exporting to other formats (pysb.export)
  • Command-line usage
  • Interactive usage
  • Implementation of specific exporters
    • Export SBML (pysb.export.sbml)
    • Export ODEs to MATLAB (pysb.export.matlab)
    • Export ODEs to Mathematica (pysb.export.mathematica)
    • Export ODEs to PottersWheel (pysb.export.potterswheel)
    • Export BNGL (pysb.export.bngl)
    • Export BNGL NET file (pysb.export.bng_net)
    • Export Kappa (pysb.export.kappa)
    • Export a “flat” PySB model (pysb.export.pysb_flat)
    • Export to StochKit (pysb.export.stochkit)
    • Export JSON (pysb.export.json)