Background to the VPH-Physiome project

To be of benefit to applications in healthcare, organ and whole organism physiology needs to be understood at both a systems level and in terms of subcellular function and tissue properties. Understanding a re-entrant arrhythmia in the heart, for example, depends on knowledge of not only numerous cellular ionic current mechanisms and signal transduction pathways, but also larger scale myocardial tissue structure and the spatial variation in protein expression. As reductionist biomedical science succeeds in elucidating ever more detail at the molecular level, it is increasingly difficult for physiologists to relate integrated whole organ function to underlying biophysically detailed mechanisms that exploit this molecular knowledge. Multi-scale computational modelling is used by engineers and physicists to design and analyse mechanical, electrical and chemical engineering systems. Similar approaches could benefit the understanding of physiological systems. To address these challenges and to take advantage of bioengineering approaches to modelling anatomy and physiology, the International Union of Physiological Sciences (IUPS) formed the Physiome Project in 1997 as an international collaboration to provide a computational framework for understanding human physiology [1].

Primary Goals

One of the primary goals of the Physiome Project [PJ04] has been to promote the development of standards for the exchange of information between models. The first of these standards, dealing with time varying but spatially lumped processes, is CellML [VarYY]. The second (dealing with spatially and time varying processes) is FieldML [CPJ09, P13] [2]. A further goal of the Physiome Project has been the development of open source tools for creating and visualizing standards-based models and running model simulations. OpenCOR is the latest in a series of software projects aimed at providing a modelling environment for CellML models. Similar tools exist for FieldML models.

Following the publication of the STEP [3] (Strategy for a European Physiome) Roadmap in 2006, the European Commission in 2007 initiated the Virtual Physiological Human (VPH) project [ea13]. A related US initiative by the Interagency Modeling and Analysis Group (IMAG) began in 2003 [4]. These projects and similar initiatives are now coordinated and are collectively referred to here as the ‘VPH-Physiome’ project [5]. The VPH-Institute [6] was formed in 2012 as a virtual organisation to providing strategic leadership, initially in Europe but now globally, for the VPH-Physiome Project.

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Footnotes

[1]

www.iups.org. The IUPS President, Denis Noble from Oxford University, and Jim Bassingthwaighte from the University of Washington in Seattle have been two of the driving forces behind the Physiome Project. Peter Hunter from the University of Auckland was appointed Chair of the newly created Physiome Commission of the IUPS in 2000. The IUPS Physiome Committee, formed in 2008, was co-chaired by Peter Hunter and Sasha Popel (JHU) and is now chaired by Andrew McCulloch from UCSD. The UK Wellcome Trust provided initial support for the Physiome Project through the Heart Physiome grant awarded in 2004 to David Paterson, Denis Noble and Peter Hunter.

[2]

CellML began as a joint public-private initiative in 1998 with funding by the US company Physiome Sciences (CEO Jeremy Levin), before being launched under IUPS as a fully open source project in 1999.

[3]

The STEP report, led by Marco Viceconte (University of Sheffield, UK), is available at www.europhysiome.org/roadmap.

[4]

This coordinates various US Governmental funding agencies involved in multi-scale bioengineering modeling 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/MultiScaleModeling/IMAG. Grace Peng of NHBIB leads the IMAG group.

[5]

Other significant contributions to the VPH-Physiome project have come from Yoshi Kurachi in Japan (www.physiome.jp), Stig Omholt in Norway (www.ntnu) and Chae-Hun Leem in Korea (www.physiome.or.kr).

[6]

www.vph-institute.org. Formed in 2012, the inaugural Director was Marco Viceconti. The current Director is Adriano Henney. The inaugural and current President of the VPH-Institute is Denis Noble.