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
)- 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
)
- Export SBML (