PEPA'd Oysters: Converting Dynamic Energy Budget Models to Bio-PEPA, illustrated by a Pacific oyster case study

Citation

Scott E, Hoyle A & Shankland C (2013) PEPA'd Oysters: Converting Dynamic Energy Budget Models to Bio-PEPA, illustrated by a Pacific oyster case study. In: Bradley J, Heljanko K, Knottenbelt W & Thomas N (eds.) volume 296. PASM'12: Sixth International Workshop on Practical Applications of Stochastic Modelling, Imperial College London, UK, 17.09.2012-17.09.2012. Elsevier, pp. 211-228. https://doi.org/10.1016/j.entcs.2013.07.014

Abstract
We present a Bio-PEPA (Biochemical-Performance Evaluation Process Algebra) computational model for the Pacific oyster, derived from a DEB (Dynamic Energy Budget) mathematical model. Experience with this specific model allows us to propose a generic scheme for translation between the widely-used DEB theory and Bio-PEPA. The benefits of translation are that a range of novel analysis tools become available, therefore improving the potential to understand complex biological phenomena at a systems level. This work also provides a link between biology, mathematics and computer science: such interlinking of disciplines is the core of the systems approach to biology.

Keywords
Dynamic Energy Budget Model; Bio-PEPA; Process Algebra; Pacific oyster (Crassostrea gigas) case study; Physiological models; Computational tools

Journal
Electronic Notes in Theoretical Computer Science: Volume 296

• PEPA'd oysters.pdf