PySB v1.10.0 Released

New features

Local functions allow PySB expressions to accept a tagged MonomerPattern or ComplexPattern as an argument. For example, in the following snippet, A synthesizes C with rate dependent on bound B:

  Observable('AB_motif', A(b=1) % B(a=1))
  Expression('f_synth', k_synthC * AB_motif(x) ** 2)
  Rule('_R1', A() @ x >> A() @ x + C(), f_synth)

See for a complete example.

  • KappaSimulator (#447)

New simulation interface for Kappa which supports multiple initial condition sets and parameter sets. Replaces pysb.kappa.run_simulation. See KappaSimulator documentation for further details.


  • Show ReusedBondError when bond connects >2 sites in a reaction pattern (#466)
  • Add dashed edge when reaction rate is an expression with observables (#458)
  • Include macros in rule._function (#451)
  • Improved error messages when external tools not found; make Atomizer use pysb.pathfinder (#460)

Bug fixes

  • Fix reading MultiState species from BioNetGen models (#462)
  • Fix Expression.get_value() (#457)
  • PySBFlatExporter now supports MultiState (#453)
  • Fix ModelNotDefinedError when self exporter is used and a model component is declared before Model() (#452)


  • Switch from coveralls to codecov (#454)