Modular modelling with Physiome standards

摘要

Key points class="unordered" style="list-style-type:disc" id="tjp7397-list-0001">The complexity of computational models is increasing, supported by research in modelling tools and frameworks. But relatively little thought has gone into design principles for complex models.We propose a set of design principles for complex model construction with the Physiome standard modelling protocol CellML.By following the principles, models are generated that are extensible and are themselves suitable for reuse in larger models of increasing complexity.We illustrate these principles with examples including an architectural prototype linking, for the first time, electrophysiology, thermodynamically compliant metabolism, signal transduction, gene regulation and synthetic biology.The design principles complement other Physiome research projects, facilitating the application of virtual experiment protocols and model analysis techniques to assist the modelling community in creating libraries of composable, characterised and simulatable quantitative descriptions of physiology.