CellML and associated tools and techniques.

Full Abstract

We have, in the last few years, witnessed the development and availability of an ever increasing number of computer models that describe complex biological structures and processes. The multi-scale and multi-physics nature of these models makes their development particularly challenging, not only from a biological or biophysical viewpoint but also from a mathematical and computational perspective. In addition, the issue of sharing and reusing such models has proved to be particularly problematic, with the published models often lacking information that is required to accurately reproduce the published results. The International Union of Physiological Sciences Physiome Project was launched in 1997 with the aim of tackling the aforementioned issues by providing a framework for the modelling of the human body. As part of this initiative, the specifications of the CellML mark-up language were released in 2001. Now, more than 7 years later, the time has come to assess the situation, in particular with regard to the tools and techniques that are now available to the modelling community. Thus, after introducing CellML, we review and discuss existing editors, validators, online repository, code generators and simulation environments, as well as the CellML Application Program Interface. We also address possible future directions including the need for additional mark-up languages.

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Author information

Author/s: Garny, Alan (A); Nickerson, David P (DP); Cooper, Jonathan (J); Weber dos Santos, Rodrigo (R); Miller, Andrew K (AK); McKeever, Steve (S); Nielsen, Poul M F (PM); Hunter, Peter J (PJ);

Affiliation: Department of Physiology, Anatomy and Genetics, University of Oxford, Sherrington Building, Parks Road, Oxford OX1 3PT, UK. alan.garny(-atsign-)dpag.ox.ac.uk

Grants: BB/E024955/1 (Agency:United Kingdom Biotechnology and Biological Sciences Research Council)

Journal and publication information

Publication Type: Journal Article; Research Support, Non-U.S. Gov't; Review

Journal: Philosophical transactions. Series A, Mathematical, physical, and engineering sciences (Philos Transact A Math Phys Eng Sci), published in England. (Language: eng)

Reference: 2008-Sep; vol 366 (issue 1878) : pp 3017-43

Dates: Created 2008/07/28; Completed 2008/09/30;

PMID: 18579471, status: MEDLINE (last retrieval date: 11/6/2008)

Sourced from the National Library of Medicine. Abstract text and other information may be subject to copyright.

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