Modelling biological modularity with CellML

In recent years advances in the construction of mathematical models of biological systems have yielded an array of valuable constructs. The authors seek to provide a ´leading practice´ method for implementing modularised kinetic mass-action models in order to obtain a number of advantages in model construction, validation and derived insights. The authors advocate the consideration of ´accounting cycles´ or ´chains´ to define ´functional´ components and the separate consideration of ´messenger´ components for mobile or diffusive molecular species. From a conceptual modularisation the authors illustrate, with an example drawn from signal transduction, a component- based formulation in the model exchange format cellular modelling markup language (CellML) 1.1 - demonstrating loose coupling between functionally-focused reusable components. Finally, the authors discuss the dilemmas associated with modelling protein-to-protein interactions, and the vision for using future CellML enhancements to resolve potential duplications when combining independently developed models.