The engineering of concurrent simulations of complex systems

Polack, Fiona; Andrews, Paul S.; Sampson, Adam T.

doi:10.1109/cec.2009.4982951

Cited by 16 publications

(18 citation statements)

References 17 publications

(16 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Polack 2014). Background and rationale for CoSMoS has been widely reported Polack 2010Polack , 2012Polack et al 2008Polack et al , 2009Polack et al , 2010, building on the first draft process, .…”

Section: Using the Cosmos Approach For Cell Proliferationmentioning

confidence: 97%

Principled simulation of cell proliferation dynamics using the CoSMoS approach

Polack

Droop

2014

Nat Comput

View full text Add to dashboard Cite

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.

show abstract

Section: Using the Cosmos Approach For Cell Proliferationmentioning

confidence: 97%

Principled simulation of cell proliferation dynamics using the CoSMoS approach

Polack

Droop

2014

Nat Comput

View full text Add to dashboard Cite

show abstract

“…Project documentation of simulation, modelling and process descriptions [44][45][46], of validation and argumentation [47][48][49], of various biological system simulation case studies [50][51][52][53], and of the CoSMoS workshop proceedings [54][55][56], is available from the CoSMoS project website 1 .…”

Section: Models and Methodsmentioning

confidence: 99%

Engineering Simulations for Cancer Systems Biology

Bown¹,

Andrews²,

Deeni³

et al. 2012

CDT

View full text Add to dashboard Cite

Abstract:Computer simulation can be used to inform in vivo and in vitro experimentation, enabling rapid, low-cost hypothesis generation and directing experimental design in order to test those hypotheses. In this way, in silico models become a scientific instrument for investigation, and so should be developed to high standards, be carefully calibrated and their findings presented in such that they may be reproduced. Here, we outline a framework that supports developing simulations as scientific instruments, and we select cancer systems biology as an exemplar domain, with a particular focus on cellular signalling models. We consider the challenges of lack of data, incomplete knowledge and modelling in the context of a rapidly changing knowledge base. Our framework comprises a process to clearly separate scientific and engineering concerns in model and simulation development, and an argumentation approach to documenting models for rigorous way of recording assumptions and knowledge gaps. We propose interactive, dynamic visualisation tools to enable the biological community to interact with cellular signalling models directly for experimental design. There is a mismatch in scale between these cellular models and tissue structures that are affected by tumours, and bridging this gap requires substantial computational resource. We present concurrent programming as a technology to link scales without losing important details through model simplification. We discuss the value of combining this technology, interactive visualisation, argumentation and model separation to support development of multi-scale models that represent biologically plausible cells arranged in biologically plausible structures that model cell behaviour, interactions and response to therapeutic interventions.

show abstract

“…A common feature of the work on critical system validation and bio-inspired or heuristic techniques is its reliance on arguments of assurance. Polack et al [29] propose argumentation for validation of agent-based simulations, complementing traditional engineering of simulations (see, for instance, the work of Sargent [33,32]). If a simulation can be argued to be a valid model of a dynamic system, then it can be used to provide evidence of the presumed behaviour of that system in different contexts.…”

Section: Validation and Assurancementioning

confidence: 99%

“…There are many definitions of a complex system. The one that is used in this chapter is based on the author's work on engineering emergent systems [28,30,29].…”

Section: Complexity and Systems Architecturesmentioning

confidence: 99%

Self-organisation for Survival in Complex Computer Architectures

Polack

2010

Lecture Notes in Computer Science

Self Cite

View full text Add to dashboard Cite

Abstract. This chapter steps back from specific self-organisational architectural solutions to consider what self-organisation means in the context of complex systems. Drawing on insights in complexity and selforganisation, the chapter explores how the natural propensity of complex systems (such as the mammalian immune system) to self-organise could be exploited as a mechanism for adaptation in complex computer architectures. Drawing on experience of immune-inspired fault-tolerant swarm robotics, the chapter speculates on how complex systems such as global information systems could adopt self-organised survivability.

show abstract

The engineering of concurrent simulations of complex systems

Cited by 16 publications

References 17 publications

Principled simulation of cell proliferation dynamics using the CoSMoS approach

Principled simulation of cell proliferation dynamics using the CoSMoS approach

Engineering Simulations for Cancer Systems Biology

Self-organisation for Survival in Complex Computer Architectures

Contact Info

Product

Resources

About