PySUNDIALS : Providing python bindings to a robust suite of mathematical tools for computational systems biology
Year: 2009
Type: dissertation
Abstract: A Python package called PySUNDIALS has been developed which provides an interface to the suite of nonlinear differential/algebraic equation solvers (SUNDIALS) using ctypes as a foreign function interface (FFI).SUNDIALS is a C implementation of a set of modern algorithms for integrating and solving various forms of the initial value problem (IVP).Additionally, arbitrary root finding capabilities, time dependent sensitivity analysis, and the solution of differential and algebraic systems are available in the various modules provided by SUNDIALS.A significant focus of the project was to ensure the python package conforms to Python language standards and syntactic expectations.Multiple examples of the SUNDIALS modules (CVODE, CVODES, IDA and KINSOL) are presented comparing PySUNDIALS to C SUNDIALS (for verification of correctness), and comparing PySUNDIALS to various other comparable software packages.The examples presented also provide benchmark comparisons for speed, and code length.Specific uses of the features of the SUNDIALS package are illustrated, including the modelling of discontinuous events using root finding, time dependent sensitivity analysis of oscillatory systems, and the modelling of equilibrium blocks using a complete set of implicit differential and algebraic equations.PySUNDIALS is available as open source software for download.It is being integrated into the systems biology software PySCeS as an optional solver set, on an ongoing basis.A brief discussion of potential methods of optimization and the continuation of the project to wrap the parallel processing modules of SUNDIALS is presented.
Author: James Gilmour Dominy
Language: English
Subfield: Modeling and Simulation
Field: Mathematics
Domain: Physical Sciences
Open Access status: green
OpenAlex ID: W804473175