Physiome Project

Discover more about the Physiome Project – a comprehensive framework for modelling the human body – and Software group.

Physiome Project

The objective of the Physiome Project of the International Union of Physiological Sciences is to provide a comprehensive framework for modelling the human body using computational methods. These methods can incorporate the biochemistry, biophysics and anatomy of cells, tissues and organs.

Led from Auckland, the international Physiome Project focuses on developing community standards, open source software and model repositories to ensure that physiological modelling has a firm foundation that will underpin healthcare across many domains. These domains include both drug development at the molecular level and medical device development at the tissue and whole body scale.

The US National Institutes of Health funded the ABI to use its Physiome Project infrastructure to map the autonomic system (sympathetic and parasympathetic nerves) from the brainstem to the visceral organs of the body. This project is aimed at a new generation of implanted stimulation devices that can compensate for loss of organ function in various disease conditions.

Research question

  • Can we develop a rational physics-based framework for physiology and clinical medicine?
    The human genome project has shown what is possible when scientists and engineers collaborate on a common goal – to provide a map of all human genes. But this is only half the story. The function of the proteins encoded by those genes is also dependent on the particular environment in which they operate and the physical laws that the physiological systems must obey.

Modelling is the only way to capture this ‘phenotype’. But biological systems are extremely complex and models must be based on standards and able to be reproduced. Examples include:

  • Interpreting physiological healthcare data from medical devices
  • Modelling drug toxicity for the FDA
  • Surgical planning. 

Software and web-accessible databases

To support that goal, the project is developing XML markup languages (CellML, FieldML) and software tools for creating, executing and visualising the output of computer models at the cell, tissue, organ and organ systems levels. It is also establishing web-accessible databases to provide the physiological information necessary to support these models.

CellML

CellML is an XML-based language designed to specify, store, and exchange models of biological systems. It is used to describe the components, and the mathematical relationships between components, of biological models.

CellML enables model builders to share models, construct models as a hierarchy of existing models, facilitating the process of model building, testing, publication, and curation. The language, based upon a relatively small number of concepts, is general enough to describe models of a wide variety of biological processes.

A repository of models is publicly available on the CellML web site. The same site also offers tools which facilitate the use of CellML, such as visual editors, simulation software, validators, and application programming interfaces for a variety of computer languages.

Browse now: The CellML Model Repository.
Find out more: CellML website.

FieldML

FieldML is typically used for the representation of 3D models, incorporating information relevant to a bioengineering context, such as:

  • Information within the volume describing tissue structure
  • Distribution of proteins and other biochemical compounds
  • Anatomical and other biological annotation.

These fields can be used to represent the dynamic geometry and solution fields of computational models at multiple scales, from cells and tissues to organs and organisms.

Visit for more information: FieldML pages at IUPS Physiome Project.

Spanning the information gap

Major developments in science and medicine are the recent explosions of information in genomics and proteomics, which are providing a plethora of information relating to the regulation of cell function. On the other hand, recent developments in imaging (using MRI, CT, PET, ultrasound and electrical mapping for instance) are providing detailed information on function at organ and organ systems.

The challenge of the Physiome project is to set up a model-based computational framework which spans this information gap. We see this as an important step toward the development of a patient-specific paradigm for diagnosis and treatment in the medicine of the future.

Funding partners

The Physiome Project gratefully acknowledges the support of its funding partners:

  • Maurice Wilkins Centre for Molecular Biodiscovery
  • Foundation for Research, Science and Technology
  • The Wellcome Trust
  • National Institutes of Health

The CellML project gratefully acknowledges the support of its funding partners:

  • Virtual Physiological Human Network of Excellence
  • Maurice Wilkins Centre for Molecular Biodiscovery
  • Physiome Project
  • @neurIST: Integrated Biomedical Informatics for the Management of Cerebral Aneurysms
  • New Zealand Institute of Mathematics & its Applications (NZIMA)
  • Foundation for Research Science & Technology (FoRST) (now Ministry of Business, Innovation & Employment)
  • Wellcome Trust
  • New Energy and Industrial Technology Development Organization (NEDO)
  • MedTechCoRE
  • Auckland Bioengineering Institute

Find out more: Physiome Project

Software Development

The Auckland Bioengineering Institute develops several software tools and frameworks to support its research activities.

OpenCMISS

OpenCMISS is a set of libraries and applications which provide the foundation for developing computational modelling and visualisation software, particularly targeting bioengineering.

OpenCMISS-Iron is a comprehensive software system for multi-physics and multi-scale bioengineering simulation. It is based on the original CMISS system, developed by the ABI over decades. Iron uses modern software development tools, and the system architecture supports both shared memory parallel processing and distributed memory parallel processing. Models and solutions are represented using FieldML. Iron is provided as a software library that can be embedded in a wide range of other software systems.

OpenCMISS-Zinc (‘Zinc’) is a cross-platform software library for building complete modelling and visualisation applications, from rich model representation to high quality OpenGL graphics rendering.

Discover more: Visit the OpenCMISS website.

Cmgui

Cmgui is a visualisation application built upon the OpenCMISS-Zinc library (see above.) It can be used for visualisation of 3D bioengineering models, including the main types of models that FieldML represents, such as the simulation result fields from CMISS and Iron. Cmgui has advanced functions for the definition of computed fields, and custom visualisations.

More information: Visit Cmgui.

PMR2

The PMR2 software system is used to provide a web accessible model repository for Physiome models. It is an open source project. PMR2 powers the Physiome model repository, where a web view is available for each model in the repository. It can be used for combined Physiome models that use multiple model representations such as CellML and FieldML.

Learn more: Visit the PMR2 webpage.

Cardiac Atlas Project

The Cardiac Atlas Project (CAP) seeks to establish a structural and functional atlas of the heart. The ABI Software Laboratory has developed the CAP database, which houses a few thousand cardiac magnetic resonance images (MRIs), and associated dynamic geometrical models of cardiac structure that have been fitted to the MRI data.

More project details: Visit Cardiac Atlas.

Members

International links

  • Australia: University of Melbourne
  • France: INRIA and CNRS
  • Ireland: Diagles-GIOME
  • Japan: Osaka University
  • UK: University of Oxford, Heriot-Watt University
  • US: University of California - San Diego (UCSD), Washington University