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

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...

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Bibliographic Details
Published in:Electronic Notes in Theoretical Computer Science
Main Authors: Scott, Erin, Hoyle, Andrew, Shankland, Carron
Other Authors: Bradley, J, Heljanko, K, Knottenbelt, W, Thomas, N, Computing Science, orcid:0000-0001-7190-1728, orcid:0000-0002-9117-7041, orcid:0000-0001-7672-2884
Format: Conference Object
Language:English
Published: Elsevier 2013
Subjects:
Dynamic Energy Budget Model
Bio-PEPA
Process Algebra
Pacific oyster (Crassostrea gigas) case study
Physiological models
Computational tools
Pacific
Crassostrea gigas
Pacific oyster
Online Access:http://hdl.handle.net/1893/16641
https://doi.org/10.1016/j.entcs.2013.07.014
http://dspace.stir.ac.uk/bitstream/1893/16641/1/PEPA%27d%20oysters.pdf
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Summary: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.

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