OpenCMISS: a multi-physics & multi-scale computational infrastructure for the VPH/Physiome project

Show simple item record Bradley, Christopher en Bowery, A en Britten, Randall en Budelmann, V en Camara, O en Christie, R en Cookson, A en Frangi, AF en Babarenda Gamage, Thiranja en Heidlauf, T en Krittian, S en Ladd, D en Little, C en Mithraratne, Premakumar en Nash, Martyn en Nickerson, David en Nielsen, Poul en Nordbø, Ø en Omholt, S en Pashaei, A en Paterson, D en Rajagopal, Vijayaraghavan en Reeve, A en Röhrle, O en Safaei, Soroush en Sebastián, R en Steghöfer, M en Wu, Tim en Yu, Yan Hei en Zhang, H en Hunter, Peter en 2011-08-16T03:34:04Z en 2011 en
dc.identifier.citation Progress in Biophysics and Molecular Biology 107(1):32-47 2011 en
dc.identifier.issn 1873-1732 en
dc.identifier.uri en
dc.description.abstract The VPH/Physiome Project is developing the model encoding standards CellML ( and FieldML ( as well as web-accessible model repositories based on these standards (models.physiome. org). Freely available open source computational modelling software is also being developed to solve the partial differential equations described by the models and to visualise results. The OpenCMISS code (, described here, has been developed by the authors over the last six years to replace the CMISS code that has supported a number of organ system Physiome projects. OpenCMISS is designed to encompass multiple sets of physical equations and to link subcellular and tissue-level biophysical processes into organ-level processes. In the Heart Physiome project, for example, the large deformation mechanics of the myocardial wall need to be coupled to both ventricular flow and embedded coronary flow, and the reactionediffusion equations that govern the propagation of electrical waves through myocardial tissue need to be coupled with equations that describe the ion channel currents that flow through the cardiac cell membranes. In this paper we discuss the design principles and distributed memory architecture behind the OpenCMISS code. We also discuss the design of the interfaces that link the sets of physical equations across common boundaries (such as fluid-structure coupling), or between spatial fields over the same domain (such as coupled electromechanics), and the concepts behind CellML and FieldML that are embodied in the OpenCMISS data structures. We show how all of these provide a flexible infrastructure for combining models developed across the VPH/Physiome community. en
dc.format.medium 1 en
dc.publisher Pergamon Press Ltd. en
dc.relation.ispartofseries Progress in Biophysics and Molecular Biology 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 en
dc.rights.uri en
dc.subject computational modelling software multi-scale multi-physics Physiome project en
dc.title OpenCMISS: a multi-physics & multi-scale computational infrastructure for the VPH/Physiome project en
dc.type Journal Article en
dc.identifier.doi 10.1016/j.pbiomolbio.2011.06.015 en
pubs.issue 1 en
pubs.begin-page 32 en
pubs.volume 107 en
dc.rights.holder Copyright: 2011 Elsevier Ltd. en
dc.identifier.pmid 21762717 en
pubs.end-page 47 en
dc.rights.accessrights en
pubs.subtype Article en
pubs.elements-id 215076 en Bioengineering Institute en ABI Associates en Engineering en Engineering Science en Science en Science Research en Maurice Wilkins Centre (2010-2014) en
pubs.record-created-at-source-date 2011-10-21 en
pubs.dimensions-id 21762717 en

Files in this item

There are no files associated with this item.

Find Full text

This item appears in the following Collection(s)

Show simple item record


Search ResearchSpace