publication . Article . 2008

BioNessie - a grid enabled biochemical networks simulation environment

Liu, X.; Jiang, J.; Ajayi, O.; Gu, X.; Gilbert, D.; Sinnott, R.O.;
Open Access English
  • Published: 01 Jan 2008
  • Publisher: IOS Press
  • Country: United Kingdom
The simulation of biochemical networks provides insight and understanding about the underlying biochemical processes and pathways used by cells and organisms. BioNessie is a biochemical network simulator which has been developed at the University of Glasgow. This paper describes the simulator and focuses in particular on how it has been extended to benefit from a wide variety of high performance compute resources across the UK through Grid technologies to support larger scale simulations.
free text keywords: QA75
Related Organizations
Download from
34 references, page 1 of 3










10. Myproxy credential management service.

11. R. Alfieri, R. Cecchini, V. Ciaschini, L. dell'Agnello, A. Gianoli, F. Spataro, F. Bonnassieux, P. Broadfoot, G. Lowe, L. Cornwall, J. Jensen, D. Kelsey, A. Frohner, D. L. Groep, W. S. de Cerff, M. Steenbakkers, G. Venekamp, D. Kouril, A. McNab, O. Mulmo, M. Silander, J. Hahkala, and K. Lhorentey. Managing dynamic user communities in a grid of autonomous resources. CHEP 2003, 2003.

12. R. Boys, D. Henderson, T. Kirkwood, D. Wilkinson, and W. E. Wolski. Calibayes: Integration of grid based simulation and data resources for bayesian calibration of biological models. BMC Bioinformatics, 6(3):14, 2005.

13. K.-H. Cho, S.-Y. Shin, H. W. Kim, O. Wolkenhauer, B. McFerran, and W. Kolch. Mathematical modeling of the influence of rkip on the erk signaling pathway. In CMSB '03: Proceedings of the First International Workshop on Computational Methods in Systems Biology, pages 127-141, London, UK, 2003. Springer-Verlag.

14. P. K. Dhar, T. C. Meng, S. Somani, L. Ye, K. Sakharkar, A. Krishnan, A. B. Ridwan, S. H. K. Wah, M. Chitre, and Z. Hao. Grid cellware: the first grid-enabled tool for modelling and simulating cellular processes. Bioinformatics, 21(7):1284- 1287, 2005.

15. D. Endy and R. Brent. Modelling cellular behaviour. Nature, 409:391-395, 2001.

34 references, page 1 of 3
Powered by OpenAIRE Research Graph
Any information missing or wrong?Report an Issue