Modular modelling with Physiome standards

作者：Cooling Michael T; Nickerson David P; Nielsen Poulm F; Hunter Peter J

来源：The Journal of Physiology, 2016, 594(23): 6817-6831.

DOI：10.1113/JP272633

The ability to produce and customise complex computational models has great potential to have a positive impact on human health. As the field develops towards whole-cell models and linking such models in multi-scale frameworks to encompass tissue, organ, or organism levels, reuse of previous modelling efforts will become increasingly necessary. Any modelling group wishing to reuse existing computational models as modules for their own work faces many challenges in the context of construction, storage, retrieval, documentation and analysis of such modules. Physiome standards, frameworks and tools seek to address several of these challenges, especially for models expressed in the modular protocol Cell ML. Aside from providing a general ability to produce modules, there has been relatively little research work on architectural principles of Cell ML models that will enable reuse at larger scales. To complement and support the existing tools and frameworks, we develop a set of principles to address this consideration. The principles are illustrated with examples that couple electrophysiology, signalling, metabolism, gene regulation and synthetic biology, together forming an architectural prototype for whole-cell modelling (including human intervention) in Cell ML. Such models illustrate how testable units of quantitative biophysical simulation can be constructed. Finally, future relationships between modular models so constructed and Physiome frameworks and tools are discussed, with particular reference to how such frameworks and tools can in turn be extended to complement and gain more benefit from the results of applying the principles.

• 出版日期2016-12-1