Process Algebra with Layers: A Language for Multi-Scale Integration Modelling

• Published in: Electronic Notes in Theoretical Computer Science
• Main Author: Scott, Erin Gemma
• Other Authors: Shankland, Carron, Hoyle, Andrew, Scottish Informatics and Computer Science Alliance (SICSA)
• Format: Doctoral or Postdoctoral Thesis
• Language: English
• Published: University of Stirling 2016
• Subjects: multi-scale models; process algebra; computational modelling; integrated scales; Multiscale modeling; Algebra; Pacific; Ocean acidification; Pacific oyster
• Online Access: http://hdl.handle.net/1893/23516; http://dspace.stir.ac.uk/bitstream/1893/23516/1/thesisErinScott.pdf

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 ...