A Primer on Modular Mass-Action Modelling with CellML

Abstract

CellML is a model exchange format designed to greatly facilitate the communication of models. Here we provide a primer on modelling mass-action kinetics with CellML and discuss some of the language features for structuring models. We illustrate these with examples of simple reactions, from which we build a basic biochemical system. We explore some best practices for structuring the models to greatly aid model reusability, as well as communication, and provide information on interacting with the CellML research community. CellML source code for the models in this chapter can be found online at the CellML model Repository (Lloyd et al. 2008), at http://models.cellml.org/workspace/modularmassactionprimer.