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The VPH-Physiome Project: Standards, tools and databases for multi-scale physiological modelling

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Modeling of Physiological Flows

Part of the book series: MS&A — Modeling, Simulation and Applications ((MS&A,volume 5))

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 important 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 visualization (cmgui and GIMIAS) or computational (OpenCMISS, OpenCell/OpenCOR and other) software.

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Notes

  1. 1.

    The concept of a “Physiome Project” was presented in a report from the Commission on Bioengineering in Physiology to the International Union of Physiological Sciences (IUPS) Council at the 32nd World Congress in Glasgow in 1993. The term “physiome” comes from “physio” (life) + “ome” (as a whole), and is intended to provide a “quantitative description of physiological dynamics and functional behaviour of the intact organism” [2, 3, 4]. A satellite workshop “On designing the Physiome Project”, organized and chaired by the Chair of the IUPS ‘Commission on Bioengineering in Physiology’ (Prof Jim Bassingthwaighte), was held in Petrodvoretz, Russia, following the 33 rd World Congress in St Petersburg in 1997. A symposium on the Physiome Project was held at the 34th World Congress of IUPS in Christchurch, New Zealand, in August 2001 and the Physiome Project was designated by the IUPS executive as a major focus for IUPS during the next decade.

  2. 2.

    This coordinates various US Governmental funding agencies involved in multi-scale bioengineering modelling research including NIH, NSF, NASA, the Dept of Energy (DoE), the Dept of Defense (DoD), the US Dept of Agriculture and the Dept of Veteran Affairs. See www.nibib.nih.gov/Research/MultiScaleModelling/IMAG.

  3. 3.

    The STEP (“Strategy for a European Physiome”) report is available at www.europhysiome. org/roadmap

  4. 4.

    See www.vph-noe.eu for details on the 15 projects funded under the VPH calls.

  5. 5.

    See www.physiome.jp for details on the Japanese Physiome Project.

  6. 6.

    www.cellml.org

  7. 7.

    www.sbml.org

  8. 8.

    www.fieldml.org

  9. 9.

    www.cellml.org/models

  10. 10.

    Interface Description Language. See www.OMG.org/cgi-bin/doc?formal/02-06-39

  11. 11.

    Distributed under a tri-licence MPL, GPL or LGPL.

  12. 12.

    Distributed under a tri-license MPL, GPL or LGPL. See also 7.

  13. 13.

    GIMIAS is released under a BSD license.

  14. 14.

    www.taverna.org.uk

  15. 15.

    All software components developed by the CAP are open source and are freely available under the Mozilla Public License Version 1.1 (mozilla.org/MPL/MPL-1.1.txt).

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Acknowledgements

The development of standards, tools and databases for the VPH/Physiome project is being funded by many public good funding agencies in Europe (e.g. the EU ICT VPH 2, 4 & 6 calls and particularly the NoE and euHeart projects), the US (the MSM Physiome RFPs) and many other countries including the UK (especially the Wellcome Trust), Japan and New Zealand. The authors thank the many people from many different groups around the globe who have contributed to the infrastructure described here – for details see the websites given for the various software projects described in the document. Funding from the Wellcome Trust for the Heart Physiome Project and the European Union for the VPH Network of Excellence (VPH NoE FP7-ICT2008-223920) and the euHeart project (VPH euHeart FP7-ICT2008-224495) is gratefully acknowledged.

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Authors and Affiliations

  1. Auckland Bioengineering Institute (ABI), University of Auckland, New Zealand

    Peter Hunter, Chris Bradley, Randall Britten, David Brooks, Richard Christie, David Ladd, Caton Little, David Nickerson, Poul Nielsen, Andrew Miller, Alistair Young & Tommy Yu

  2. Department of Physiology, Anatomy and Genetics (DPAG), University of Oxford, UK

    Peter Hunter, Chris Bradley & Alan Garny

  3. Center for Computational Imaging and Simulation Technologies in Biomedicine (CISTIB), Universitat Pompeu Fabra, Barcelona, Spain

    Luigi Carotenuto, Alejandro Frangi, Xavier Planes & Martin Steghoffer

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  1. Peter Hunter
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Correspondence to Peter Hunter .

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Editors and Affiliations

  1. MOX - Department of Mathematics, Politecnico di Milano, Italy

    Davide Ambrosi  & Alfio Quarteroni  & 

  2. Mathematics Institute of Computational Science and Engineering, École Polytechnique Fédérale de Laussane, Switzerland

    Alfio Quarteroni  & Gianluigi Rozza  & 

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Hunter, P. et al. (2012). The VPH-Physiome Project: Standards, tools and databases for multi-scale physiological modelling. In: Ambrosi, D., Quarteroni, A., Rozza, G. (eds) Modeling of Physiological Flows. MS&A — Modeling, Simulation and Applications, vol 5. Springer, Milano. https://doi.org/10.1007/978-88-470-1935-5_8

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