CellML: its future, present and past

Prog Biophys Mol Biol. Jun-Jul 2004;85(2-3):433-50. doi: 10.1016/j.pbiomolbio.2004.01.004.

Abstract

Advances in biotechnology and experimental techniques have lead to the elucidation of vast amounts of biological data. Mathematical models provide a method of analysing this data; however, there are two issues that need to be addressed: (1) the need for standards for defining cell models so they can, for example, be exchanged across the World Wide Web, and also read into simulation software in a consistent format and (2) eliminating the errors which arise with the current method of model publication. CellML has evolved to meet these needs of the modelling community. CellML is a free, open-source, eXtensible markup language based standard for defining mathematical models of cellular function. In this paper we summarise the structure of CellML, its current applications (including biological pathway and electrophysiological models), and its future development--in particular, the development of toolsets and the integration of ontologies.

Publication types

  • Review

MeSH terms

  • Algorithms*
  • Animals
  • Cell Physiological Phenomena*
  • Computer Simulation / standards*
  • Computer Simulation / trends
  • Humans
  • Hypermedia / standards*
  • Hypermedia / trends
  • Information Storage and Retrieval / methods*
  • Information Storage and Retrieval / standards
  • Information Storage and Retrieval / trends
  • Models, Biological*
  • Programming Languages*
  • Software / standards*
  • Software / trends