PySB documentation¶
PySB is a framework for building mathematical rule-based models of biochemical systems as Python programs. PySB abstracts the complex process of creating equations describing interactions among multiple proteins (or other biomolecules) into a simple and intuitive domain specific language embedded within Python. PySB accomplishes this by automatically generating sets of BNGL or Kappa rules and using the rules for simulation or analysis. PySB makes it straightforward to divide models into modules and to call libraries of reusable elements (macros) that encode standard biochemical actions. These features promote model transparency, reuse and accuracy. PySB interoperates with standard scientific Python libraries such as NumPy, SciPy and SymPy to enable model simulation and analysis.
Contents:
- Installation
- Tutorial
- Frequently Asked Questions
- PySB Modules Reference
- PySB core (
pysb.core)ANYCompartmentCompartmentAlreadySpecifiedErrorComplexPatternComponentComponentDuplicateNameErrorComponentSetConstantExpressionErrorDanglingBondErrorDuplicateMonomerErrorDuplicateSiteErrorEnergyPatternExpressionExpressionErrorInitialInitialConditionsViewInvalidComplexPatternExceptionInvalidComponentNameErrorInvalidInitialConditionErrorInvalidReactionPatternExceptionInvalidReversibleSynthesisDegradationRuleMatchOnce()ModelModelExistsWarningModelNotDefinedErrorMonomerMonomerPatternMultiStateObservableOdeViewParameterReactionPatternRedundantSiteConditionsErrorReusedBondErrorRuleRuleExpressionSelfExporterSymbolExistsWarningTagTagAlreadySpecifiedErrorUnknownSiteErrorWILDas_complex_pattern()as_reaction_pattern()build_rule_expression()extract_site_conditions()is_state_bond_tuple()validate_const_expr()validate_expr()
- 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)assemble_chain_sequential_base()assemble_pore_sequential()bind()bind_complex()bind_table()bind_table_complex()catalyze()catalyze_complex()catalyze_one_step()catalyze_one_step_reversible()catalyze_state()degrade()drug_binding()equilibrate()pore_bind()pore_transport()synthesize()synthesize_degrade_table()
- 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)
- PySB core (
- Useful References