Using CellML with OpenCMISS to simulate multi-scale physiology

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dc.contributor.author Nickerson, David en
dc.contributor.author Ladd, D en
dc.contributor.author Razak Jainulabdeen, Jagir en
dc.contributor.author Safaei, Soroush en
dc.contributor.author Suresh, Vinod en
dc.contributor.author Hunter, Peter en
dc.contributor.author Bradley, Christopher en
dc.contributor.editor McKeever, S en
dc.date.accessioned 2015-05-08T03:47:58Z en
dc.date.issued 2015 en
dc.identifier.citation Frontiers in Bioengineering and Biotechnology, 2015, 2, 10 pp. en
dc.identifier.uri http://hdl.handle.net/2292/25442 en
dc.description.abstract OpenCMISS is an open-source modeling environment aimed, in particular, at the solution of bioengineering problems. OpenCMISS consists of two main parts: a computational library (OpenCMISS-Iron) and a field manipulation and visualisation library (OpenCMISS-Zinc). OpenCMISS is designed for the solution of coupled multi-scale, multi-physics problems in a general-purpose parallel environment. CellML is an XML format designed to encode biophysically based systems of ordinary differential equations and both linear and non-linear algebraic equations. A primary design goal of CellML is to allow mathematical models to be encoded in a modular and reusable format to aide reproducibility and interoperability of modeling studies. In OpenCMISS we make use of CellML models to enable users to configure various aspects of their multi-scale physiological models. This avoids the need for users to be familiar with the OpenCMISS internal code in order to perform customised computational experiments. Examples of this are: cellular electrophysiology models embedded in tissue electrical propagation models; material constitutive relationships for mechanical growth and deformation simulations; time-varying boundary conditions for various problem domains; fluid constitutive relationships and lumped parameter models. In this paper we provide implementation details describing how CellML models are integrated into multi-scale physiological models in OpenCMISS. The external interface OpenCMISS presents to users will also be described, including specific examples exemplifying the extensibility and usability these tools provide the physiological modelling and simulation community. We conclude with some thoughts on future extension of OpenCMISS to make use other community developed information standards, such as FieldML, SED-ML, and BioSignalML. Plans for the integration of accelerator code (GPU and FPGA) generated from CellML models is also discussed. en
dc.relation.ispartofseries Frontiers in Bioengineering and Biotechnology en
dc.rights Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated. Previously published items are made available in accordance with the copyright policy of the publisher. Details obtained from http://www.sherpa.ac.uk/romeo/issn/2296-4185/ en
dc.rights.uri https://researchspace.auckland.ac.nz/docs/uoa-docs/rights.htm en
dc.rights.uri http://creativecommons.org/licenses/by/4.0/ en
dc.title Using CellML with OpenCMISS to simulate multi-scale physiology en
dc.type Journal Article en
dc.identifier.doi 10.3389/fbioe.2014.00079 en
pubs.volume 2 en
dc.description.version VoR - Version of Record en
dc.identifier.pmid 25601911 en
pubs.author-url http://journal.frontiersin.org/Journal/10.3389/fbioe.2014.00079/abstract en
pubs.publication-status Published en
dc.rights.accessrights http://purl.org/eprint/accessRights/OpenAccess en
pubs.subtype Article en
pubs.elements-id 464215 en
pubs.org-id Bioengineering Institute en
pubs.org-id ABI Associates en
pubs.org-id Engineering en
pubs.org-id Engineering Science en
pubs.org-id Science en
pubs.org-id Science Research en
pubs.org-id Maurice Wilkins Centre (2010-2014) en
dc.identifier.eissn 2296-4185 en
pubs.number 79 en
pubs.record-created-at-source-date 2014-12-03 en
pubs.dimensions-id 25601911 en


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