Integrating Biosystem Models Using Waveform Relaxation. (21st December 2008)

• Record Type: Journal Article
• Authors: Li, Linzhong; Seymour, Robert M.; Baigent, Stephen
• Other Names: Goutsias John Academic Editor.
• Is Part Of: EURASIP journal on bioinformatics and systems biology. Volume 2008(2008)
• Publication Date: 2008-12-21
• Subjects: Bioinformatics -- Periodicals; Systems biology -- Periodicals; Systems Biology; Signal Processing, Computer-Assisted; Bio-informatique; Biologie systémique; Bioinformatics; Systems biology; Systems Biology; Bioinformatics; Electronic journals; Periodical; Fulltext; Internet Resources; Periodicals; Periodicals; 570.285
• DOI: 10.1155/2008/308623
• Languages: English
• ISSNs: 1687-4145

Abstract

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.