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Appears in Collections:Computing Science and Mathematics eTheses
Title: Process Algebra with Layers: A Language for Multi-Scale Integration Modelling
Author(s): Scott, Erin Gemma
Supervisor(s): Shankland, Carron
Hoyle, Andrew
Keywords: multi-scale models
process algebra
computational modelling
integrated scales
Issue Date: 4-Apr-2016
Publisher: University of Stirling
Citation: E. Scott, A. Hoyle and C. Shankland. PEPA'd Oysters: Converting Dynamic Energy Budget Models to Bio-PEPA, illustrated by a Pacific oyster case study. In the proceedings of the Sixth International Workshop on the Practical Application of Stochastic Modelling (PASM) and the Eleventh International Workshop on Parallel and Distributed Methods in Verification (PDMC), J. Bradley, K. Heljanko, W. Knottenbelt and N. Thomas (Eds.), ENTCS 296, pp. 211-228, 2013. DOI: 10.1016/j.entcs.2013.07.014
Abstract: Multi-scale modelling and analysis is becoming increasingly important and relevant. Analysis of the emergent properties from the interactions between scales of multi-scale systems is important to aid in solutions. There is no universally adopted theoretical/computational framework or language for the construction of multi-scale models. Most modelling approaches are specific to the problem that they are addressing and use a hybrid combination of modelling languages to model specific scales. This thesis addresses if process algebra can offer a unique opportunity in the definition and analysis of multi-scale models. In this thesis the generic Process Algebra with Layers (PAL) is defined: a language for multi-scale integration modelling. This work highlights the potential of process algebra to model multi-scale systems. PAL was designed based on features and challenges found from modelling a multi-scale system in an existing process algebra. The unique features of PAL are the layers: Population and Organism. The novel language modularises the spatial scales of the system into layers, therefore, modularising the detail of each scale. An Organism can represent a molecule, organelle, cell, tissue, organ or any organism. An Organism is described by internal species. An internal species, dependent on the scale of the Organism, can also represent a molecule, organelle, cell, tissue, organ or any organism. Populations hold specific types of Organism, for example, life stages, cell phases, infectious states and many more. The Population and Organism layers are integrated through mirrored actions. This novel language allows the clear definition of scales and interactions within and between these scales in one model. PAL can be applied to define a variety of multi-scale systems. PAL has been applied to two unrelated multi-scale system case studies to highlight the advantages of the generic novel language. Firstly the effects of ocean acidification on the life stages of the Pacific oyster. Secondly the effects of DNA damage from cancer treatment on the length of a cell cycle and cell population growth.
Type: Thesis or Dissertation

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