Scott E, Hoyle A & Shankland C (2016) Process Algebra with Layers: A Language for Multi-scale Integration Modelling, Illustrated by a Cell Cycle and DNA Damage Case Study. In: Bracciali A & Caravagna G (eds.) Proceedings of Computational Intelligence Methods for Bioinformatics and Biostatistics. 13th International Conference on Computational Intelligence methods for Bioinformatics and Biostatistics, Stirling, 01.09.2016-03.09.2016. Stirling: University of Stirling, pp. 240-246. http://www.cs.stir.ac.uk/events/cibb2016/index.html
Abstract We present a novel process algebra designed for multi-scale integration modelling: Process Algebra with Layers (PAL). The unique features of PAL are the integrated layers: Population and Organism. The novel language modularises the spatial scales of the system into layers, therefore, modularising the detail of each scale. Populations hold specific types of Organism, for example, life stages, cell phases, infectious states and many more. An example illustrates how the algebra can be used to model and simulate the multi-scale system of cell growth and damage from cancer treatment. Results of the PAL model are compared to wet laboratory survival fractions of cells given different doses of radiation treatment . This comparison shows how PAL can be used to aid in investigations of cancer treatment in systems biology.
Keywords Process Algebra; Multi-scale; Modelling; Cell Cycle; Cancer