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
  • Option 1: Install PySB natively on your computer
    • Recommended additional software
  • Option 2: Docker container with PySB and Jupyter Notebook
    • Background
    • Install Docker and the PySB software stack
    • Important notes for Docker installations
• Tutorial
  • Introduction
  • First steps
  • Creating a model
  • Using a model
  • Model creation in depth
    • Component
    • Monomer
    • Parameter
    • Rules
    • Observables
  • Initial conditions
  • Simulation and analysis
  • Visualization
  • Higher-order rules
  • Using provided macros
  • Compartments
  • Model calibration
  • Modules
  • Miscellaneous
    • Self-export
• Frequently Asked Questions
  • General
  • Rule and Reaction Rate Laws
  • Simulation
• PySB Modules Reference
  • PySB core (pysb.core)
    • ANY
    • Compartment
    • CompartmentAlreadySpecifiedError
    • ComplexPattern
    • Component
    • ComponentDuplicateNameError
    • ComponentSet
    • ConstantExpressionError
    • DanglingBondError
    • DuplicateMonomerError
    • DuplicateSiteError
    • EnergyPattern
    • Expression
    • ExpressionError
    • Initial
    • InitialConditionsView
    • InvalidComplexPatternException
    • InvalidComponentNameError
    • InvalidInitialConditionError
    • InvalidReactionPatternException
    • InvalidReversibleSynthesisDegradationRule
    • MatchOnce()
    • Model
    • ModelExistsWarning
    • ModelNotDefinedError
    • Monomer
    • MonomerPattern
    • MultiState
    • Observable
    • OdeView
    • Parameter
    • ReactionPattern
    • RedundantSiteConditionsError
    • ReusedBondError
    • Rule
    • RuleExpression
    • SelfExporter
    • SymbolExistsWarning
    • Tag
    • TagAlreadySpecifiedError
    • UnknownSiteError
    • WILD
    • as_complex_pattern()
    • as_reaction_pattern()
    • build_rule_expression()
    • extract_site_conditions()
    • is_state_bond_tuple()
    • validate_const_expr()
    • validate_expr()
  • ODE integrators (pysb.integrate)
    • Solver
    • odesolve()
  • Simulation tools (pysb.simulator)
    • BngSimulator
    • CudaSSASimulator
    • CupSodaSimulator
    • KappaSimulator
    • OpenCLSSASimulator
    • PopulationMap
    • ScipyOdeSimulator
    • SimulationResult
    • StochKitSimulator
  • Set/get paths for external tools (pysb.pathfinder)
    • get_path()
    • list_programs()
    • set_path()
  • Testing PySB Models (pysb.testing.modeltests)
    • AllObservablesInRules
    • ModelAssertion
    • ModelAssertionFailure
    • ReactionAssertion
    • ReactionNetworkAssertion
    • RuleAssertion
    • SpeciesAssertion
    • SpeciesDoesNotExist
    • SpeciesExists
    • SpeciesIsProduct
    • SpeciesIsReactant
    • SpeciesNeverProduct
    • SpeciesNeverReactant
    • SpeciesOnlyProduct
    • SpeciesOnlyReactant
    • TestSuite
  • BioNetGen integration (pysb.bng)
    • BngBaseInterface
    • BngConsole
    • BngFileInterface
    • BngInterfaceError
    • NoInitialConditionsError
    • NoRulesError
    • generate_equations()
    • generate_network()
    • load_equations()
    • parse_bngl_expr()
    • run_ssa()
    • set_bng_path()
  • Kappa integration (pysb.kappa)
    • KasaInterfaceError
    • KasimInterfaceError
    • SimulationResult
    • StaticAnalysisResult
    • contact_map()
    • influence_map()
    • run_simulation()
    • run_static_analysis()
    • set_kappa_path()
  • 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)
    • FilterPredicate
    • Function
    • Module
    • Name
    • Pattern
    • ReactionPatternMatcher
    • RulePatternMatcher
    • SpeciesPatternMatcher
    • check_dangling_bonds()
    • get_bonds_in_pattern()
    • get_half_bonds_in_pattern()
    • match_complex_pattern()
    • match_reaction_pattern()
    • monomers_from_pattern()
  • Visualizing model structure
    • Render a model’s reaction network (pysb.tools.render_reactions)
    • Render a model’s species (pysb.tools.render_species)
  • Sensitivity anaylsis (pysb.tools.sensitivity_analysis)
    • InitialsSensitivity
    • PairwiseSensitivity
    • cartesian_product()
  • Importing from other formats (pysb.importers)
    • model_from_bngl()
    • model_from_biomodels()
    • model_from_sbml()
    • sbml_translator()
  • Exporting to other formats (pysb.export)
    • Command-line usage
    • Interactive usage
    • Implementation of specific exporters
    • CompartmentsNotSupported
    • CustomSympyFunctionsNotSupported
    • EnergyNotSupported
    • ExportError
    • Exporter
    • ExpressionsNotSupported
    • FeatureNotSupportedError
    • LocalFunctionsNotSupported
    • export()
    • pad()
• Useful References
  • Python Language
  • NumPy and SciPy
  • BioNetGen

Indices and tables

• Index

• Module Index

• Search Page