PyDSTool

The PyDSTool software environment is designed to develop, simulate, and analyze
dynamical systems models, particularly for biological applications. Unlike the
engineering application focus and graphical specification environments of most
general purpose simulation tools, PyDSTool provides a programmatic environment
well suited to exploratory data- and hypothesis-driven biological modeling
problems. In this work, we show how the environment facilitates the application
of hybrid dynamical modeling to the reverse engineering of complex biophysical
dynamics; in this case, of an excitable membrane. The example demonstrates how
the software provides novel tools that support the inference and validation of
mechanistic hypotheses and the inclusion of data constraints in both quantitative
and qualitative ways. The biophysical application is broadly relevant to models
in the biosciences. The open source and platform-independent PyDSTool package is
freely available under the BSD license from
http://sourceforge.net/projects/pydstool/. The hosting service provides links to
documentation and online forums for user support.

Hybrid models and biological model reduction with PyDSTool.

PyDSTool is a tool to simulate and explore data- and hypothesis-driven biophysical dynamics models for biological applications, such as ODEs, DAEs, maps, and hybrid systems.

PyDSTool

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