Stellenbosch University

Description of organisation

Stellenbosch University (SUN) is ranked as one of the top research intensive universities of South Africa. The university hosts a number of center’s of excellence: UNESCO Associated Centre for Macromolecules & Materials; The National Institute for Theoretical Physics (NITheP) Centre for Renewable and Sustainable Energy Studies; Nepad Water Initiative; DST/NRF Centre of Excellence for Biomedical TB Research (CBTBR); DST/NRF Centre for Invasion Biology (CIB); and the South African Centre for Epidemiological Modelling & Analysis (SACEMA).

The university's overall research goals are formulated in the HOPE project, “Science for society”, where a multidisciplinary approach rooted in science enables excellent research on local, regional and African challenges. Promoting human dignity and health is one of the research focuses within the HOPE project.

Previous experience

Prof Snoep is holder of the SARCHi (South African Research Chair initiative) chair for “Mechanistic modelling of health and epidemiology” and works in close collaboration with SACEMA and the Biochemistry department at SUN. The research chair uses a constrained based hierarchical modelling approach to bridge the steps from drug target to whole body disease states and epidemiology for malaria, HIV/TB, and diabetes type II. In 2000 Snoep started JWS Online, one of the first web accessible model databases and has maintained and expanded this initiative ever since. JWS Online is used in several Systems Biology projects, such as SysMO, The Virtual Liver, and Unicellsys and is linked to international scientific journals for the reviewing and hosting of mathematical models. Snoep has been involved in the development of model description and annotation standards and in his group several detailed kinetic models have been constructed and experimentally validated.

Profile of staff members

Prof J.L. Snoep is holder of the SARCHi (South African Research Chair initiative) chair for “Mechanistic modelling of health and epidemiology” and works in close collaboration with SACEMA and the Biochemistry department at SUN. Snoep’s expertise is in mechanistic modelling of metabolism, with a strong experimental approach for model construction and validation. He has ample experience in software development for web based model simulations, modelling standards and data management.

Dr. A. Welte is director of the South African Centre for Epidemiological Modelling & Analysis (SACEMA). He is a physicist by training, and is interested in a diverse range of projects involving the mathematical modelling of biological, chemical and population‑dynamic processes.

Dr. D. van Niekerk is a physicist from training, working at Stellenbosch University as an expert modeler in Systems Biology projects.

Webpage

http://www.sun.ac.za/

Five recent publications relevant to the project

Geenen, S., du Preez, F.B., Reed, M., Nijhout, H.F., Kenna, J.G., Wilson, I.D., Westerhoff, H.V. and Snoep, J.L. (2012) A mathematical modelling approach to assessing the reliability of biomarkers of glutathione metabolism. European Journal of Pharmaceutical Sciences 46: 233‑243.

Kolodkin A, Boogerd FC, Plant N, Bruggeman FJ, Goncharuk V, Lunshof J, Moreno‑Sanchez R, Yilmaz N, Bakker BM, Snoep JL, Balling R, Westerhoff HV. (2012) Emergence of the silicon human and network targeting drugs. European Journal of Pharmaceutical Sciences 46: 190‑197.

Swat, M., Kielbasa, S.M., Polak, S., Olivier, B.G., Bruggeman, F.B., Quinton Tulloch, M., Snoep, J.L., Verhoeven, A.J., and Westerhoff, H.V. (2011) What it takes to understand and cure a living system: computational systems biology and a systems biology‑driven pharmacokinetics‑ pharmacodynamics platform. Interface focus 1, 16‑23.

Kolodkin AN, Bruggeman FJ, Plant N, Moné MJ, Bakker BM, Campbell MJ, van Leeuwen JPTM, Carlberg C, Snoep JL, Westerhoff HV. (2010) Design principles of nuclear receptor signaling: how complex networking improves signal transduction. Molecular Systems Biology, 6, 446.

Le Novere, N., et al., Snoep, J. L., Kohn, K., and Kitano, H. (2009) The Systems Biology Graphical Notation. Nature Biotechnology 27: 735‑41