title: Web-based applications for building, managing and analysing kinetic models of biological systems.
abstract: 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.
authors.affiliation: Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117576. cheld@nus.edu.sg
authors.forename: Dong-Yup
authors.initials: DY
authors.lastname: Lee
authors.forename: Rajib
authors.initials: R
authors.lastname: Saha
authors.forename: Faraaz Noor Khan
authors.initials: FN
authors.lastname: Yusufi
authors.forename: Wonjun
authors.initials: W
authors.lastname: Park
authors.forename: Iftekhar A
authors.initials: IA
authors.lastname: Karimi
mesh_terms: D019295:Computational Biology; D003198:Computer Simulation; D016208:Databases, Factual; D006801:Humans; D020407:Internet; D008433:Mathematics; D008954:Models, Biological; D012984:Software; D014584:User-Computer Interface