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Briefings in Bioinformatics Advance Access published online on September 19, 2008
Briefings in Bioinformatics, doi:10.1093/bib/bbn039
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© The Author 2008. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Web-based applications for building, managing and analysing kinetic models of biological systems

Dong-Yup Lee, Rajib Saha, Faraaz Noor Khan Yusufi, Wonjun Park and Iftekhar A. Karimi

Corresponding author. Dong-Yup Lee, Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117576. Tel: +65 6478 8900; Fax: +65 6778 1936; E-mail: cheld{at}nus.edu.sg

Mathematical modelling and computational analysis play an essential role in improving our capability to elucidate the functions and characteristics of complex biological systems such as metabolic, regulatory and cell signalling pathways. The modelling and concomitant simulation render it possible to predict the cellular behaviour of systems under various genetically and/or environmentally perturbed conditions. This motivates systems biologists/bioengineers/bioinformaticians to develop new tools and applications, allowing non-experts to easily conduct such modelling and analysis. However, among a multitude of systems biology tools developed to date, only a handful of projects have adopted a web-based approach to kinetic modelling. In this report, we evaluate the capabilities and characteristics of current web-based tools in systems biology and identify desirable features, limitations and bottlenecks for further improvements in terms of usability and functionality. A short discussion on software architecture issues involved in web-based applications and the approaches taken by existing tools is included for those interested in developing their own simulation applications.

Keywords: systems biology, web-based applications, kinetic modelling, dynamic simulation

Submitted: April 22, 2008. Received (in revised form): August 15, 2008.


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