PySB
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  • Installation
  • Tutorial
  • Frequently Asked Questions
  • 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
    • Sensitivity anaylsis (pysb.tools.sensitivity_analysis)
    • Importing from other formats (pysb.importers)
    • Exporting to other formats (pysb.export)
  • Useful References
PySB
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  • PySB Modules Reference
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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)
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© Copyright 2012, C. F. Lopez, J. L. Muhlich, J. A. Bachman Revision 8819eaa8.

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