PySB v1.4.0 Released

New features

  • StochKitSimulator, an interface to the stochastic simulator StochKit. See pysb.simulator.stochkit.StochKitSimulator.
  • InitialsSensitivity, a tool to perform pairwise sensitivity analysis of initial conditions. See EXPERIMENTAL.
  • Import models directly from BioModels from just their ID (BIOMDxxx... or MODELxxx...) with pysb.importers.sbml.model_from_biomodels().

General improvements

  • Faster simulation runs for models with many expressions (~60x speedup for a 200-expression model).
  • Improved accuracy and better error reporting when parsing SBML expressions in pysb.importers.sbml.
  • The Kappa interface has been upgraded to support Kappa version 4. This also means Kappa v3 is no longer supported.


  • CupSodaSimulator now works on Python 3.
  • Simulators now fully respect parameter value overrides for initial condition parameters (#252).
  • Simulators now allow overriding a non-zero initial condition to zero (#251).
  • Simulators no longer have problems with parameter names that are unicode objects (still only ASCII characters are allowed, though) (#278).
  • Model components with the same name as a top-level sympy object (anything you would see in from sympy import *) no longer cause errors when simulating (#259).
  • Applying a compartment condition to a MonomerPattern that already has one now correctly raises an exception (#258).
  • PysbFlatExporter now works with compartments using inline size declarations (#210).
  • ComplexPattern.is_equivalent_to now correctly handles certain combinations of compartments that were previously mishandled (#257).