Reusing simulation experiment specifications in developing models by successive composition — a case study of the Wnt/β-catenin signaling pathway. (August 2017)

• Record Type: Journal Article
• Authors: Peng, Danhua; Warnke, Tom; Haack, Fiete; Uhrmacher, Adelinde M
• Is Part Of: Simulation. Volume 93:Number 8(2017)
• Page Start: 659
• Page End: 677
• Publication Date: 2017-08
• Subjects: Simulation experiments -- model composition -- experiment specification -- semantic validation; Computer simulation -- Periodicals; 003.3
• DOI: 10.1177/0037549717704314
• Languages: English
• ISSNs: 0037-5497

Abstract

With the increasing size and complexity of models, developing models by composing existing ones becomes more important. We exploit the idea of reusing simulation experiments of individual models for composition to automatically generate experiments for the composed model. First, we illustrate the process of modeling based on composition and discuss the role simulation experiments can play in this process. Our focus is on semantic validation of the composed model. We explicitly specify simulation experiments in simulation experiment specification via a Scala layer, including the desired model behavioral properties and their required experiment set-ups. Models are annotated with experiment specifications, and upon composition, these specifications are adapted and automatically executed for the composed model. The approach is applied in a case study of developing a Wnt/ β -catenin signaling pathway model by successively composing three individual models, where we exploit metric interval temporal logic to describe model behavioral properties and check averages of stochastic simulation results against these properties.