Engineering Simulations as Scientific Instruments: A Pattern Language With Kieran Alden, Paul S. Andrews, James L. Bown, Alastair Droop, Richard B. Greaves, Mark Read, Adam T. Sampson, Jon Timmis, Alan F.T. Winfield

This book describes CoSMoS (Complex Systems Modelling and Simulation), a pattern-based approach to engineering trustworthy simulations that are both scientifically useful to the researcher and scientifically credible to third parties. This approach emphasises three key aspects to this development of a simulation as a scientific instrument: the use of explicit models to capture the scientific domain, the engineered simulation platform, and the experimental results of running simulations; the use of arguments to provide evidence that the scientific instrument is fit for purpose; and the close co-working of domain scientists and simulation software engineers.

In Part I the authors provide a managerial overview: the rationale for and benefits of using the CoSMoS approach, and a small worked example to demonstrate it in action. Part II is a catalogue of the core patterns. Part III lists more specific “helper” patterns, showing possible routes to a simulation. Finally Part IV documents CellBranch, a substantial case study developed using the CoSMoS approach.

Part I, Overview of the CoSMoS Approach.- CoSMoS: Rationale and Concepts.- What’s In It for Me?.- The CoSMoS Approach in Miniature.- Part II, The Core CoSMoS Pattern Language.- The CoSMoS Simulation Pattern.- Discovery Phase Patterns: Building the Domain Model.- Development Phase Patterns: Developing the Platform.- Exploration Phase Patterns: Using the Platform.- Structured Argumentation Patterns.- Part III, The CoSMoS Helper Patterns.- Modelling and Documentation Patterns.- Real-World Simulation Patterns.- Part IV, CellBranch Case Study.- Introduction to the CellBranch Simulation.- CellBranch: Increment 1: Single Transcription Factor.- CellBranch: Increment 1: Discovery Phase.- CellBranch: Increment 1: Development Phase.- CellBranch: Increment 1: Exploration Phase.- CellBranch: Increment 2: Multiple Transcription Factors.- CellBranch: Increment 2: Discovery Phase.- CellBranch: Increment 2: Development Phase.- CellBranch: Increment 2: Exploration Phase.- CellBranch: Lessons and Code.