From isolation to integration, a systems biology approach for building the Silicon Cell

Abstract

In the last decade, the field now commonly referred to as systems biology has de- veloped rapidly. With the sequencing of whole genomes and the development of analysis methods to measure many of the cellular components, we have now en- tered the realm of complete descriptions at a cellular level. Although we have been seeing that larger and larger systems were being described, making a description complete is much more important than just adding additional components. The possibility of making complete descriptions will cause a paradigm shift in our ap- proaches, on a theoretical, as well as a modeling and an experimental level. We will here present our view on systems biology and specifically focus on modeling strategies to build cellular models on the basis of detailed enzyme kinetic informa- tion: an approach advocated in the Silicon Cell project (http://www.siliconcell.net) making use of the JWS Online database of kinetic models (http://jjj.biochem.sun.ac.za).