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  1. PySB v1.7.0 Released

    New Features

    • Python 3.7 now officially supported (in addition to 3.6 and 2.7) (#368)
    • Filtering for ComponentSets (documentation) (#340)
    • SBML export now uses LibSBML and supports compartments and expressions (#367)
    • On demand observable trajectories without adding them to the model (documentation) (#337)

    General Improvements

    • The <> operator for …
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  2. PySB v1.6.0 Released

    New Features

    • New reversible rule operator |; the previous <> operator is now pending deprecation (#309)
    • Saving and loading of SimulationResult objects with metadata in HDF5 format (#292)
    • PySB now supports Kappa 4, including custom rate laws with PySB Expressions. Kappa 3 support has been dropped (#334)
    • Rule pattern matching and …
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  3. PySB v1.5.0 Released

    New features

    BngSimulator, an interface to all simulators provided by BioNetGen: ODE, partitioned-leaping, SSA (stochastic) and NFsim (network-free stochastic). See pysb.simulator.bng.BngSimulator (#272).

    General improvements

    • Faster and more memory-efficient construction of ODEs from rules (#293).
    • ScipyOdeSimulator is faster in "pure Python" mode (i.e. without weave and a …
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  4. 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 pysb.tools.sensitivity_analysis.InitialSensitivity. EXPERIMENTAL.
    • Import models directly from BioModels from just their ID (BIOMDxxx... or MODELxxx...) with pysb.importers.sbml.model_from_biomodels().

    General …

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  5. PySB v1.3.0 Released

    New features

    • CupSodaSimulator, a wrapper for the cupSODA GPU-based ODE integrator. No special Python libraries are necessary since cupSODA comes as a standalone binary, but if PyCUDA is installed then PySB can auto-detect the configuration details of your GPU. See the documentation in pysb.simulator.CupSodaSimulator for more.
    • Simulators can …
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  6. PySB v1.2.0 Released

    New features

    Brand new Simulator classes and SimulationResult classes in the pysb.simulator package. The old pysb.integrate API is unchanged but has been reimplemented using the Simulator class. Model import from other types of models in the pysb.importers package. Currently supports BNGL and SBML model import.


    • pysb_flat …
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  7. PySB v1.1.0 Released

    PySB has officially adopted semantic versioning. This means v1.1.0 includes new features as compared to v1.0.x, but is still backwards compatible so you won't have to change any of your models to upgrade to it.

    New features

    • Full Python 3 compatibility. All tests pass under Python …
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