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  3. PySB v1.14.0 Released

    New features

    • Energy modeling by @jmuhlich in #553 This adds support for BNG's energy modeling formalism. Models can now contain EnergyPatterns as well as energy-based Rules with the Arrhenius rate law parameterized by activation energy (E₀) and rate distribution (φ). Energy-based models can be simulated directly in PySB or exported …
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  6. PySB v1.13.0 Released

    Removed features

    • Remove pure-python exporter (#543). The pure Python exporter was a legacy feature to export a PySB model for use without PySB itself. We recommend using a virtual environment or container as a better alternative (e.g. Ananconda, Docker). Users requiring this feature who cannot use alternatives could copy …
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  7. PySB v1.11.1 Released

    The only change in this release is that Python version requirements are now specified in setup.py metadata (Python 2.7, or >=3.5). This is anticipated to be the final PySB release to support Python 2.7.

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  8. PySB v1.12.0 Released

    This version of PySB supports Python 3.6-3.9. Python 2.7 is no longer supported.

    New features

    • Implement reversible synthesis rules (#499)

    Improvements

    • ScipyOdeSimulator speedup through refactoring, use of partial (#531, #483)
    • Use double precision for BNG and Kappa parameters (#490)
    • Allow constant expressions for compartment sizes (#525)
    • Faster …
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  9. PySB v1.11.0 Released

    New features

    • JSON model import and export (#469)

    Improvements

    • Models stored in HDF5 files using SimulationResult.save() now use JSON, rather than pickle
    • Raise a ValueError if a rule defined with reverse rate, but expression is not reversible (#471)

    Bug fixes

    • Fixes for importing certain BNGL and SBML models which …
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  10. 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))
  Tag('x')
  Expression('f_synth', k_synthC * AB_motif …
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  11. PySB v1.9.1 Released

    Bug fixes

    • Fix BngSimulator when specifying parameters to change initial conditions (#450)

    Miscellaneous

    • Use Anaconda package of LibSBML on Python 3.7 for testing on Travis (#448)
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  12. PySB v1.9.0 Released

    New Features

    • MultiState capability, which enables a single Monomer site to be specified with multiple states (documentation) (#410)
    • ScipyOdeSimulator multiprocessing capability, using n_processors argument (documentation) (#395)
    • Multi-GPU simulations and chunking support (split large simulation sets into GPU-sized blocks) for CupSodaSimulator (#409)
    • Sensitivity analysis class can now work for model parameter …
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  13. PySB v1.8.1 Released

    Bugfixes

    • Fix path detection for external tools in new Anaconda releases (#394)
    • Fix errors in tutorials and example models (#392)
    • Fix error message in ScipyOdeSimulator referring to renamed kwarg (#391)
    • Fix package name for libsbml in setup.py (#390)
    • Tests: Fix Python 3.7 libsbml installation on travis (#388)
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  14. PySB v1.8.0 Released

    New Features

    • Model component names will now tab-complete when accessed as part of a ComponentSet (#380

    General Improvements

    • Keyword arguments to __init__ are now validated by ScipyOdeSimulator (#381), StochKitSimulator (#382), and CupSodaSimulator (#383)
    • BioNetGen: Extra functions are now supported, including And, Or, Floor, Ceiling, Min, Max, Abs, and the constants …
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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  22. 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.

    Bugfixes

    • pysb_flat …
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  24. 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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