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 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.
KeywordsMarkup Language DICOM Standard Model Repository Document Object Model Physiome Project
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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