The JWS Online Project

JWS Online aims to provide a service to the Systems Biology community by 1) giving access to a database of curated models of biological systems, and 2) allowing the users to run these models in a web browser via an easy to use interface, and 3) helping in reviewing of manuscripts containing kinetic models. In addition to this service role, JWS Online is an important component of an ambitious research initiative: The Silicon Cell. Whereas as a service JWS Online is a repository of published models, in the research activity models are not stored as published but are changed to reflect standardized notation of metabolites and enzymes, and a direct link between model and experimental data is provided.

The JWS Online team

JWS Online was started in 2000 by Jacky Snoep and Brett Olivier, just to try and run simulations in a browser and to make curated models available for everyone. Currently Brett works on his stand-alone simulation tool (PySCeS) while Jacky continued working on JWS Online, now together with Carel van Gend as full-time programmer and Riaan Conradie, Franco du Preez, DuToit Schabbort, Gerald Penkler and Francois du Toit helping out with coding models and Kora Holm making the metabolic schemes. In Amsterdam and Manchester mirror sites of JWS Online are set up and maintained by Cor Stoof and Steve O'Hagan respectively. Cor works in the team as Java programmer on the applet code. Hans Westerhoff is one of the drivers behind the Silicon Cell project which is closely connected to JWS Online more..

The Inner Workings

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Collaborations

The JWS Online team works together with other model databases (Biomodels, SABIO-RK), Systems Biology initiatives (The Silicon Cell, SBML, YSBN, HepatoSys, ESCEC), simulation engines (PySCeS, Copasi), and scientific journals (Microbiology, FEBS J, IET Systems Biology and Metabolomics). more..

Funding

The South African National Bioinformatics Network funds the JWS Online project, providing with infrastructure, student bursaries (Riaan, Franco and Gerald) and a postdoc salary (Carel). more..

Publications

JWS Online and the Silicon Cell project have been described in a number of publications, see more.. When citing JWS Online, please refer to: B.G. Olivier and J.L. Snoep (2004), Web-based kinetic modelling using JWS Online, Bioinformatics 20, 2143-2144.