The VPH-Physiome Project: Standards, tools and databases for multi-scale physiological modelling
The VPH/Physiome project is developing tools and model databases for computational physiology based on three primary model encoding standards: CellML, SBML and FieldML. For the modelling community these standards are the equivalent of the DICOM standard f
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The VPH-Physiome Project: standards, tools and databases for multi-scale physiological modelling Peter Hunter, Chris Bradley, Randall Britten, David Brooks, Luigi Carotenuto, Richard Christie, Alejandro Frangi, Alan Garny, David Ladd, Caton Little, David Nickerson, Poul Nielsen, Andrew Miller, Xavier Planes, Martin Steghoffer, Alistair Young, and Tommy Yu
Abstract. The VPH/Physiome project is developing tools and model databases for computational physiology based on three primary model encoding standards: CellML, SBML and FieldML. For the modelling community these standards are the equivalent of the DICOM standard for the clinical imaging community and it is imPeter Hunter ( ) and Chris Bradley Auckland Bioengineering Institute (ABI), University of Auckland, New Zealand and Department of Physiology, Anatomy and Genetics (DPAG), University of Oxford, United Kingdom e-mail: [email protected] Randall Britten and David Brooks Auckland Bioengineering Institute (ABI), University of Auckland, New Zealand Luigi Carotenuto Center for Computational Imaging and Simulation Technologies in Biomedicine (CISTIB), Universitat Pompeu Fabra, Barcelona, Spain Richard Christie Auckland Bioengineering Institute (ABI), University of Auckland, New Zealand Alejandro Frangi Center for Computational Imaging and Simulation Technologies in Biomedicine (CISTIB), Universitat Pompeu Fabra, Barcelona, Spain Alan Garny Department of Physiology, Anatomy and Genetics (DPAG), University of Oxford, United Kingdom David Ladd, Caton Little, David Nickerson, Poul Nielsen and Andrew Miller Auckland Bioengineering Institute (ABI), University of Auckland, New Zealand Xavier Planes, Martin Steghoffer Center for Computational Imaging and Simulation Technologies in Biomedicine (CISTIB), Universitat Pompeu Fabra, Barcelona, Spain Alistair Young and Tommy Yu Auckland Bioengineering Institute (ABI), University of Auckland, New Zealand
Ambrosi D., Quarteroni A., Rozza G. (Eds.): Modeling of Physiological Flows. DOI 10.1007/978-88-470-1935-5 8, © Springer-Verlag Italia 2012
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portant that the tools adhere to these standards to ensure that models from different groups can be curated, annotated, reused and combined. This chapter discusses the development and use of the VPH/Physiome standards, tools and databases, and also discusses the minimum information standards and ontology-based metadata standards that are complementary to the markup language standards. Data standards are not as well developed as the model encoding standards (with the DICOM standard for medical image encoding being the outstanding exception) but one new data standard being developed as part of the VPH/Physiome suite is BioSignalML and this is described here also. The PMR2 (Physiome Model Repository 2) database for CellML and FieldML files is also described, together with the Application Programming Interfaces (APIs) that facilitate access to the models from the visualisation (cmgui and GIMIAS) or computational (OpenCMISS, OpenCell/OpenCOR and other) software.
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