title: Modelling biological modularity with CellML.
abstract: 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.
authors.affiliation: Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand. m.cooling@auckland.ac.nz
authors.forename: M T
authors.initials: MT
authors.lastname: Cooling
authors.forename: P
authors.initials: P
authors.lastname: Hunter
authors.forename: E J
authors.initials: EJ
authors.lastname: Crampin
mesh_terms: D000465:Algorithms; D022082:Cellular Structures / Q000378:metabolism; D016247:Information Storage and Retrieval; D007295:Inositol Phosphates / Q000378:metabolism; D007700:Kinetics; D008954:Models, Biological; D054799:Phospholipase C beta / Q000378:metabolism; D011381:Programming Languages; D043562:Receptors, G-Protein-Coupled / Q000378:metabolism; D015398:Signal Transduction; D049490:Systems Biology / Q000379:methods; D013598:Systems Theory
chemical_list: D007295:Inositol Phosphates; D043562:Receptors, G-Protein-Coupled; C092449:inositol 1,2,3-trisphosphate; D054799:Phospholipase C beta