PySUNDIALS : Providing python bindings to a robust suite of mathematical tools for computational systems biology
Date
2009-03
Authors
Dominy, James Gilmour
Journal Title
Journal ISSN
Volume Title
Publisher
Stellenbosch : University of Stellenbosch
Abstract
A Python package called PySUNDIALS has been developed which provides
an interface to the suite of nonlinear di erential/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
nding capabilities, time dependent sensitivity analysis, and the solution of
di erential and algebraic systems are available in the various modules provided
by SUNDIALS. A signi cant 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 veri cation
of correctness), and comparing PySUNDIALS to various other comparable
software packages. The examples presented also provide benchmark comparisons
for speed, and code length. Speci c uses of the features of the SUNDIALS
package are illustrated, including the modelling of discontinuous events using
root nding, time dependent sensitivity analysis of oscillatory systems, and
the modelling of equilibrium blocks using a complete set of implicit di erential
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.
Description
Thesis (MSc (Biochemistry))--University of Stellenbosch, 2009.
Keywords
Python, Sundials, Metabolic models, Kinetic models, Systems biology, Biological systems -- Computer simulation, Biological systems -- Mathematical models, Dissertations -- Biochemistry, Theses -- Biochemistry