JWS online cellular systems modelling and microbiology.

Rapid developments in the relatively new disciplines of ‘bioinformatics’, ‘computational biology’ and ‘systems biology’ have led to a marked increase in the use of kinetic models in the study of complex biological systems [for example, see ‘Nature insight: Computational biology’ (2002) Nature 420, 205–251]. When reading publications in these ‘new’ fields, it is easy to overlook the fact that there exists a long-standing tradition of using kinetic models in biology. In the 1960s, pioneers such as Chance, Garfinkel, Higgins and Hess (e.g. Chance et al., 1960) had already begun using kinetic models to explore biochemical systems. Since that time, running computer simulations has become easier. Faster personal computers and the development of dedicated simulation software have removed many of the numerical and computational obstacles to building and running kinetic models. Nevertheless, the construction of kinetic models, especially of detailed ‘silicon cell’ type models (http://www.siliconcell.net/) (e.g. Bakker et al., 1997; Mulquiney & Kuchel, 1999; Teusink et al., 2000; Hoefnagel et al., 2002), can still be a tedious and time-consuming process. Considering the hard work involved in building such detailed kinetic models, it is rather surprising that so little attention is paid to presentation and conservation of existing kinetic models. Thus, no official repository of kinetic models currently exists and no standard method of presentation of kinetic models in scientific literature has been agreed upon. A number of initiatives have been started to collect kinetic models, such as the CellML (http://www.cellml.org) and SBML (http://www.sbw-sbml.org/) databases which have similar, but not identical, goals. Both projects use XML-based exchange formats. While CellML strives to describe the structure and underlying mathematics of cellular models in a very general way, SBML aims to be a generic platform for exchanging pathway and model reaction information between several existing applications. SBML compatibility is already integrated into several metabolic modelling packages, for example, SCAMP (Sauro, 1993), GEPASI (Mendes, 1997) and JARNAC (Sauro, 2000). However, neither of these databases is complete yet and the chances of finding ‘the interesting model’ that you have just read about in the literature are not necessarily good. Although a published model description should be sufficient for one to build the kinetic model, this could still be a daunting task since many model descriptions contain errors, are not complete or, due to a lack of a model description standard, are vague.