Physiome Project

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

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 the CellML Model Repository.
Find out more about the project on the CellML website.

The CellML project gratefully acknowledges the support of its funding partners, who are listed at the bottom of this page.

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.

For more information, visit the FieldML pages on the IUPS Physiome Project website.

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:

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

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

To find out more about the Physiome Project on an international level

Visit the Physiome Project website.

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Auckland Bioengineering Institute