Principled simulation of cell proliferation dynamics using the CoSMoS approach

Polack, Fiona; Droop, Alastair

Abstract

A collaboration between cancer biologists and academic software engineers has been exploring the development of an agent-based simulator to inform and support work on the dynamics of cell proliferation in the study of prostate disorders. The research has influenced and been informed by the CoSMoS project. This paper presents the simulation project (which is not yet complete). We reflect on the reality of following CoSMoS principles; we describe the domain exploration and show how software modelling approaches (here, Petri nets, state diagrams) can be used to express both biological and software models. We explore fitness for purpose and consider ways to present a fitness argument. We consider issues in choosing simulation media and mapping from domain models through to code. The implementation emphasis is on traceability to support reuse and extension of the simulator, as well as demonstrable fitness for purpose. Initial work on calibration is presented. We discuss the calibration results, that both support and challenge the design and assumptions captured in the domain modelling and development activities.

Citation

Polack, F., & Droop, A. (2014). Principled simulation of cell proliferation dynamics using the CoSMoS approach. Natural Computing, 14(1), 63-82. https://doi.org/10.1007/s11047-014-9468-z

• Journal Article Type: Article
• Online Publication Date: Oct 17, 2014
• Publication Date: 2014-03
• Deposit Date: Mar 17, 2023
• Journal: Natural Computing
• Print ISSN: 1567-7818
• Electronic ISSN: 1572-9796
• Publisher: Springer
• Peer Reviewed: Peer Reviewed
• Volume: 14
• Issue: 1
• Pages: 63-82
• DOI: https://doi.org/10.1007/s11047-014-9468-z
• Keywords: Cell proliferation; Agent-based simulation; CoSMoS; Modelling and simulation
• Public URL: https://hull-repository.worktribe.com/output/4241728