Research output

Conference Paper (in Formal Publication) ()

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 (ed.), Elsevier. PASM'12: Sixth International Workshop on Practical Applications of Stochastic Modelling, 17.9.2012 - 17.9.2012, Imperial College London, UK, Electronic Notes in Theoretical Computer Science, 296, pp. 211-228.

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

StatusPublished
EditorBradley J, Heljanko K, Knottenbelt W, Thomas N
AuthorsScott Erin, Hoyle Andrew, Shankland Carron
Publication date16/08/2013
Date of public distribution17/09/2012
URLhttp://www.sciencedirect.com/…1571066113000455
PublisherElsevier
ISSN 1571-0661
LanguageEnglish

Journal
Electronic Notes in Theoretical Computer Science: Volume 296

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