CellML and associated tools and techniques
Open Access
- 25 June 2008
- journal article
- review article
- Published by The Royal Society in Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences
- Vol. 366 (1878), 3017-3043
- https://doi.org/10.1098/rsta.2008.0094
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.Keywords
This publication has 20 references indexed in Scilit:
- Reference descriptions of cellular electrophysiology modelsBioinformatics, 2008
- Experience reportACM SIGPLAN Notices, 2007
- Cell model for efficient simulation of wave propagation in human ventricular tissue under normal and pathological conditionsPhysics in Medicine & Biology, 2006
- The Noble cardiac ventricular electrophysiology models in CellMLProgress in Biophysics and Molecular Biology, 2006
- SUNDIALSACM Transactions on Mathematical Software, 2005
- Computer model of action potential of mouse ventricular myocytesAmerican Journal of Physiology-Heart and Circulatory Physiology, 2004
- CellML: its future, present and pastProgress in Biophysics and Molecular Biology, 2004
- An Overview of CellML 1.1, a Biological Model Description LanguageSIMULATION, 2003
- One‐Dimensional Rabbit Sinoatrial Node Models:Journal of Cardiovascular Electrophysiology, 2003
- The Virtual Cell: a software environment for computational cell biologyTrends in Biotechnology, 2001