Biological systems modelling
JWS Online is a Systems Biology tool for the construction, modification and simulation of kinetic models and for the storage of curated models.
JWS Online is a Systems Biology tool for the construction, modification and simulation of kinetic models and for the storage of curated models.
With the new JWS Online model builder you can build a model from scratch using a simple interface. Models can be simulated directly in the JWS Online simulator. The builder adheres very closely to the SBML model specification and supports the MIRIAM and SBO standards for annotation, and provides a useful online annotation tool.
Simulate curated kinetic models from the JWS Online database, or non-curated models built or uploaded to JWS Online. JWS Online supports time evolutions, steady-state simulations, structural analysis, metabolic-control analysis, parameter scans, and reaction plots.
JWS Online now uses a database implementation with a native format that mirrors the SBML specification. This minimises changes in SBML structure during the upload-edit-save cycle. JWS Online supports uploading and modification of existing models in SBML or JWS format.
JWS Online aims to provide a service to the systems biology community by:
JWS Online was created in 2000 by Jacky Snoep and Brett Olivier with the simple goal of making curated systems biology models accessible to everyone through a browser-based model simulator. Currently Brett works on his stand-alone Python modelling tools (PySCeS and PySCeS-CBM), while Jacky continues to direct the development of JWS Online, with Carl Christensen and Dawie van Niekerk as the current developers. Dawie van Niekerk and Kathleen Green are also currently responsible for curating the JWS model database. Daniel Palm, Johann Eicher, Martin Peters and Franco Du Preez have contributed significantly to the development of JWS Online and the simulation backend. Riaan Conradie, Du Toit Schabbort, Kora Holm, Francois du Toit, Stefan Kühn and Carla Breytenbach have contributed significantly to the curation of models and the construction of model schemas. Mirror sites of JWS Online are maintained in Amsterdam by Cor Stoof and in Manchester by Stuart Owen.
JWS Online is designed to interface with other model databases (Biomodels, SABIO-RK), systems biology initiatives (SysMO-SEEK, The Silicon Cell Project, YSBN, HepatoSys, ESCEC), simulation engines (PySCeS, Copasi), and scientific journals (Microbiology, FEBS J, IET Systems Biology and Metabolomics). Additionally, JWS Online is compliant with recognised systems biology standards and languages, including Miriam, SBML and SED-ML. JWS Online collaborates with Hans Westerhoff's research group at the Vrije Universiteit Amsterdam, and the Triple-J Group for Molecular Cell Physiology at the University of Stellenbosch.
JWS Online has been funded by The South African National Bioinformatics Network (NBN) and the National Research Foundation, specifically the South African Research Chairs Initiative (SARChI). The Biotechnology and Biological Sciences Research Council (BBSRC) has provided funding for data management in SysMO.
JWS Online and the Silicon Cell project have been described in a number of publications. 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.
