Integrating Biosystem Models Using Waveform Relaxation |
| |
| Authors: | Linzhong Li RobertM Seymour Stephen Baigent |
| |
| Affiliation: | 1Institute for Energy Technology (IFE), P.O. Box 40, 2027 Kjeller, Norway;2Department of Mathematics, University College London, Gower Street, London WC1E 6BT, UK;3Center for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, Wolfson House, 4 Stephenson Way, London NW1 2HE, UK |
| |
| Abstract: | Modelling in systems biology often involves the integration of component models into larger composite models. How to do this systematically and efficiently is a significant challenge: coupling of components can be unidirectional or bidirectional, and of variable strengths. We adapt the waveform relaxation (WR) method for parallel computation of ODEs as a general methodology for computing systems of linked submodels. Four test cases are presented: (i) a cascade of unidirectionally and bidirectionally coupled harmonic oscillators, (ii) deterministic and stochastic simulations of calcium oscillations, (iii) single cell calcium oscillations showing complex behaviour such as periodic and chaotic bursting, and (iv) a multicellular calcium model for a cell plate of hepatocytes. We conclude that WR provides a flexible means to deal with multitime-scale computation and model heterogeneity. Global solutions over time can be captured independently of the solution techniques for the individual components, which may be distributed in different computing environments. |
| |
| Keywords: | |
|
|
