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. JWS Online is linked to a number or research initiatives: SysMO-DB, The Virtual Liver, and UniCellSys, and universities and research institutes: Stellenbosch University, Vrije Universiteit Amsterdam, Manchester University and the Centre for Plant Integrative Biology. In addition JWS Online is an important component of an ambitious research initiative: The Silicon Cell.
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. Brett has moved away from the project and works on his stand-alone simulation tool (PySCeS) while Jacky continued working on JWS Online, initially together with Carel van Gend as full-time programmer which was replaced by Franco du Preez in 2009. On and off post grad students in the lab help with coding models, notably Riaan Conradie, Gerald Penkler and Francois du Toit Kora Holm have helped, also by drawing metabolic schemes. SBML support for JWS Online was developed in collaboration with Andreas Weideman and Ursula Kummer. In Amsterdam and Manchester mirror sites of JWS Online are set up and at these sites we have been helped by Cor Stoof (VU), Steve O'Hagan and Neil Swainston (University of Manchester) respectively. Cor has worked in the team as Java programmer on the applet code, to which Neil Swainston has made a large contribution as well. We are working on adding MIRIAM annotation to the models, and Falko Krause has helped by making semantic SBML available for JWS Online queries. Hans Westerhoff is one of the drivers behind the Silicon Cell project which is closely connected to JWS Online more..
The Inner Workings
more..Collaborations
The JWS Online
team works together with other model databases and repositories for kinetic information (Biomodels,
SABIO-RK), Systems Biology initiatives (The Silicon Cell,
YSBN, HepatoSys, ESCEC, The Virtual Liver, UniCellSys, SysMO), simulation engines (PySCeS,
Copasi), and scientific journals (Microbiology, FEBS J, IET
Systems Biology and Metabolomics). We try to adhere to and help developing Systems Biology standards (SBML, SBGN, MIRIAM, SEDML).more..
Funding
The South African National Bioinformatics Network (2004-2009) has funded the JWS Online project, providing with infrastructure, and student bursaries. Currently JWS Online (Franco du Preez and Jacky Snoep at Manchester) funds JWS Online as part of the SysMO-DB team. 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.