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PyDSTool Description
PyDSTool is a Python-based tool that is aimed at providing a powerful suite of computational tools for the development, simulation, and analysis of dynamical systems. This systems are used for the modeling of physical processes in many scientific disciplines. The emphasis is placed on the support of data analysis as part of the process of data-driven modeling. The focus is maintained on models involving ordinary differential equations (ODEs), differential-algebraic equations (DAEs), and discrete maps. Main features: Efficient and state-of-the-art ODE / DAE / discrete map simulation tools (using dynamically-linked and automatically generated C code, if external compiler available) (see Generators) Hybrid model and event-driven simulation support (HybridSystems) Simulations and analysis can be forced to be "bounds safe", e.g. for "non-negativity preservation" (see BoundsSafety) Bifurcation analysis and continuation tools in-built, via PyCont Support for data-driven modeling (see DataDrivenModels) Interactive command-line / script-based interface "Index-free" and context-heavy data structures, including an enhanced version of arrays (see Pointsets) Symbolic expression utilities (including evaluation, substitution, derivatives, some simplification) (see Symbolic) Easy to build complex models using hierarchical object-oriented data structures that contain composable model specifications (see ModelSpec) Memory management utilities, data import & export (including SBML conversion and LaTeX markup via the SloppyCell package - see that page for details) Modular code design allows easy expansion to support other algorithms (contributions welcome) Data structures and toolkits for parameter estimation / model fitting and other time-series and data-driven problems (see Parameter Estimation) Seamless use with tools in SciPy, Numpy, etc. through dynamic typing Additional toolboxes for specific applications, including biomechanical modeling, computational neuroscience, and systems biology (see ToolboxDocumentation) Many tutorial examples and documentation available online at this Wiki
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