Full Text Available
Note: Clicking the button above will open the full text document at the original institutional repository in a new window.
PySUNDIALS : Providing python bindings to a robust suite of mathematical tools for computational systems biology
Thesis (MSc (Biochemistry))--University of Stellenbosch, 2009.
Saved in:
| Main Author: | |
|---|---|
| Other Authors: | |
| Format: | Thesis |
| Language: | English |
| Published: |
Stellenbosch : University of Stellenbosch
2009
|
| Subjects: | |
| Tags: |
No Tags, Be the first to tag this record!
|
| _version_ | 1867613932050448384 |
|---|---|
| access_status_str | Open Access |
| author | Dominy, James Gilmour |
| author2 | Hofmeyr, J.-H. S. |
| author_browse | Dominy, James Gilmour Hofmeyr, J.-H. S. |
| author_facet | Hofmeyr, J.-H. S. Dominy, James Gilmour |
| author_sort | Dominy, James Gilmour |
| collection | Thesis |
| dc_rights_str_mv | University of Stellenbosch |
| description | Thesis (MSc (Biochemistry))--University of Stellenbosch, 2009. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/2029 |
| institution | Stellenbosch University (South Africa) |
| language | English |
| last_indexed | 2026-06-10T12:43:59.926Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2009 |
| publishDateRange | 2009 |
| publishDateSort | 2009 |
| publisher | Stellenbosch : University of Stellenbosch |
| publisherStr | Stellenbosch : University of Stellenbosch |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/2029 PySUNDIALS : Providing python bindings to a robust suite of mathematical tools for computational systems biology Dominy, James Gilmour Hofmeyr, J.-H. S. Rohwer, J. M. University of Stellenbosch. Faculty of Science. Dept. of Biochemistry. Python Sundials Metabolic models Kinetic models Systems biology Biological systems -- Computer simulation Biological systems -- Mathematical models Theses -- Biochemistry Dissertations -- Biochemistry Thesis (MSc (Biochemistry))--University of Stellenbosch, 2009. 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. 2009-02-26T14:11:05Z 2010-06-01T08:39:09Z 2009-02-26T14:11:05Z 2010-06-01T08:39:09Z 2009-03 Thesis http://hdl.handle.net/10019.1/2029 en University of Stellenbosch application/pdf Stellenbosch : University of Stellenbosch |
| spellingShingle | Python Sundials Metabolic models Kinetic models Systems biology Biological systems -- Computer simulation Biological systems -- Mathematical models Theses -- Biochemistry Dissertations -- Biochemistry Dominy, James Gilmour PySUNDIALS : Providing python bindings to a robust suite of mathematical tools for computational systems biology |
| title | PySUNDIALS : Providing python bindings to a robust suite of mathematical tools for computational systems biology |
| title_full | PySUNDIALS : Providing python bindings to a robust suite of mathematical tools for computational systems biology |
| title_fullStr | PySUNDIALS : Providing python bindings to a robust suite of mathematical tools for computational systems biology |
| title_full_unstemmed | PySUNDIALS : Providing python bindings to a robust suite of mathematical tools for computational systems biology |
| title_short | PySUNDIALS : Providing python bindings to a robust suite of mathematical tools for computational systems biology |
| title_sort | pysundials providing python bindings to a robust suite of mathematical tools for computational systems biology |
| topic | Python Sundials Metabolic models Kinetic models Systems biology Biological systems -- Computer simulation Biological systems -- Mathematical models Theses -- Biochemistry Dissertations -- Biochemistry |
| url | http://hdl.handle.net/10019.1/2029 |
| work_keys_str_mv | AT dominyjamesgilmour pysundialsprovidingpythonbindingstoarobustsuiteofmathematicaltoolsforcomputationalsystemsbiology |