Journal article

Modular assembly of dynamic models in systems biology

Michael Pan, Peter J Gawthrop, Joseph Cursons, Edmund J Crampin

PLOS COMPUTATIONAL BIOLOGY | PUBLIC LIBRARY SCIENCE | Published : 2021

Abstract

It is widely acknowledged that the construction of large-scale dynamic models in systems biology requires complex modelling problems to be broken up into more manageable pieces. To this end, both modelling and software frameworks are required to enable modular modelling. While there has been consistent progress in the development of software tools to enhance model reusability, there has been a relative lack of consideration for how underlying biophysical principles can be applied to this space. Bond graphs combine the aspects of both modularity and physics-based modelling. In this paper, we argue that bond graphs are compatible with recent developments in modularity and abstraction in system..

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Grants

Awarded by Australian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology


Funding Acknowledgements

This research was in part conducted and funded by the Australian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology (project number CE140100036, http://purl.org/au-research/grants/arc/CE140100036), awarded to EJC. MP was supported by a Postdoctoral Research Fellowship from the School of Mathematics and Statistics, University of Melbourne. PJG was supported by the Faculty of Engineering and Information Technology, University of Melbourne via a Professorial Fellowship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.