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Volume 7

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Reaction Kinetics
Data



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In Silico Biology 7 S1, 04 (2007); ©2007, Bioinformation Systems e.V.  



Data and model integration using JWS Online

Carel van Gend1, Riaan Conradie1, Franco B. du Preez1 and Jacky L. Snoep1, 2 *

1 Triple J Group for Molecular Cell Physiology, Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa.
2 Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK

* Corresponding author
   Email: jls@sun.ac.za


Edited by I. Rojas and U. Wittig (guest editors); received and accepted March 21, 2007; published March 27, 2007


Abstract

Systems Biology requires a tight integration of experimental data and detailed computer models to obtain a quantitative understanding of the system under study. To facilitate this integration a standardization of data and model representation and storage is important. We illustrate here such an integration using JWS Online, the modeling tool developed in our group. We follow the approach of the Silicon Cell project for the construction and validation of kinetic models and discuss some issues with respect to storage of experimental data and models. The majority of the published kinetic models for biological systems have been developed for metabolic networks and this will be our focus in this manuscript. It is not our aim to present here an all encompassing method for data and model integration, but rather to present our work on this topic to start a discussion in which the different initiatives, methods and tools can be compared.


Keywords: JWS Online, Silicon Cell, kinetic model, database