TY - JOUR
T1 - Towards building the silicon cell
T2 - A modular approach
AU - Snoep, Jacky L.
AU - Bruggeman, Frank
AU - Olivier, Brett G.
AU - Westerhoff, Hans V.
PY - 2006/2
Y1 - 2006/2
N2 - Systems Biology aims to understand quantitatively how properties of biological systems can be understood as functions of the characteristics of, and interactions between their macromolecular components. Whereas, traditional biochemistry focused on isolation and characterization of cellular components, the challenge for Systems Biology lies in integration of this knowledge and the knowledge about molecular interactions. Computer models play an important role in this integration. We here discuss an approach with which we aim to link kinetic models on small parts of metabolism together, so as to form detailed kinetic models of larger chunks of metabolism, and ultimately of the entire living cell. Specifically, we will discuss techniques that can be used to model a sub-network in isolation of a larger network of which it is a part, while still maintaining the dynamics of the larger complete network. We will start by outlining the JWS online system, the silicon cell project, and the type of models we propose. JWS online is a model repository, which can be used for the storage, simulation and analysis of kinetic models. We advocate to integrate a top-down approach, where measurements on the complete system are used to derive fluxes in a detailed structural model, with a bottom-up approach, consisting of the integration of molecular mechanism-based detailed kinetic models into the structural model.
AB - Systems Biology aims to understand quantitatively how properties of biological systems can be understood as functions of the characteristics of, and interactions between their macromolecular components. Whereas, traditional biochemistry focused on isolation and characterization of cellular components, the challenge for Systems Biology lies in integration of this knowledge and the knowledge about molecular interactions. Computer models play an important role in this integration. We here discuss an approach with which we aim to link kinetic models on small parts of metabolism together, so as to form detailed kinetic models of larger chunks of metabolism, and ultimately of the entire living cell. Specifically, we will discuss techniques that can be used to model a sub-network in isolation of a larger network of which it is a part, while still maintaining the dynamics of the larger complete network. We will start by outlining the JWS online system, the silicon cell project, and the type of models we propose. JWS online is a model repository, which can be used for the storage, simulation and analysis of kinetic models. We advocate to integrate a top-down approach, where measurements on the complete system are used to derive fluxes in a detailed structural model, with a bottom-up approach, consisting of the integration of molecular mechanism-based detailed kinetic models into the structural model.
KW - Detailed kinetic model
KW - JWS online
KW - Model repository
KW - Systems biology
UR - http://www.scopus.com/inward/record.url?scp=32044435851&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=32044435851&partnerID=8YFLogxK
U2 - 10.1016/j.biosystems.2005.07.006
DO - 10.1016/j.biosystems.2005.07.006
M3 - Article
C2 - 16242236
AN - SCOPUS:32044435851
SN - 0303-2647
VL - 83
SP - 207
EP - 216
JO - BioSystems
JF - BioSystems
IS - 2-3 SPEC. ISS.
ER -