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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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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spelling ftunivstirling:oai:dspace.stir.ac.uk:1893/16641 2023-05-15T15:58:23+02:00 PEPA'd Oysters: Converting Dynamic Energy Budget Models to Bio-PEPA, illustrated by a Pacific oyster case study Scott, Erin Hoyle, Andrew Shankland, Carron 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 2013-08-16 application/pdf 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 en eng Elsevier 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. Bradley J (Editor), Heljanko K (Editor), Knottenbelt W (Editor) & Thomas N (Editor) PASM'12: Sixth International Workshop on Practical Applications of Stochastic Modelling, Imperial College London, UK, 17.09.2012-17.09.2012. Electronic Notes in Theoretical Computer Science, 296, pp. 211-228. https://doi.org/10.1016/j.entcs.2013.07.014 http://homepages.cs.ncl.ac.uk/nigel.thomas/PASM12.htm#publication http://hdl.handle.net/1893/16641 doi:10.1016/j.entcs.2013.07.014 WOS:000216919300014 2-s2.0-84883387223 687726 http://dspace.stir.ac.uk/bitstream/1893/16641/1/PEPA%27d%20oysters.pdf This article is open-access. Open access publishing allows free access to and distribution of published articles where the author retains copyright of their work by employing a Creative Commons attribution licence. Proper attribution of authorship and correct citation details should be given. http://creativecommons.org/licenses/by-nc-nd/4.0/ CC-BY CC-BY-NC-ND Dynamic Energy Budget Model Bio-PEPA Process Algebra Pacific oyster (Crassostrea gigas) case study Physiological models Computational tools Conference Paper VoR - Version of Record 2013 ftunivstirling https://doi.org/10.1016/j.entcs.2013.07.014 2022-06-13T18:45:03Z 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. Conference Object Crassostrea gigas Pacific oyster University of Stirling: Stirling Digital Research Repository Pacific Electronic Notes in Theoretical Computer Science 296 211 228
institution Open Polar
collection University of Stirling: Stirling Digital Research Repository
op_collection_id ftunivstirling
language English
topic Dynamic Energy Budget Model
Bio-PEPA
Process Algebra
Pacific oyster (Crassostrea gigas) case study
Physiological models
Computational tools
spellingShingle Dynamic Energy Budget Model
Bio-PEPA
Process Algebra
Pacific oyster (Crassostrea gigas) case study
Physiological models
Computational tools
Scott, Erin
Hoyle, Andrew
Shankland, Carron
PEPA'd Oysters: Converting Dynamic Energy Budget Models to Bio-PEPA, illustrated by a Pacific oyster case study
topic_facet Dynamic Energy Budget Model
Bio-PEPA
Process Algebra
Pacific oyster (Crassostrea gigas) case study
Physiological models
Computational tools
description 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.
author2 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
author Scott, Erin
Hoyle, Andrew
Shankland, Carron
author_facet Scott, Erin
Hoyle, Andrew
Shankland, Carron
author_sort Scott, Erin
title PEPA'd Oysters: Converting Dynamic Energy Budget Models to Bio-PEPA, illustrated by a Pacific oyster case study
title_short PEPA'd Oysters: Converting Dynamic Energy Budget Models to Bio-PEPA, illustrated by a Pacific oyster case study
title_full PEPA'd Oysters: Converting Dynamic Energy Budget Models to Bio-PEPA, illustrated by a Pacific oyster case study
title_fullStr PEPA'd Oysters: Converting Dynamic Energy Budget Models to Bio-PEPA, illustrated by a Pacific oyster case study
title_full_unstemmed PEPA'd Oysters: Converting Dynamic Energy Budget Models to Bio-PEPA, illustrated by a Pacific oyster case study
title_sort pepa'd oysters: converting dynamic energy budget models to bio-pepa, illustrated by a pacific oyster case study
publisher Elsevier
publishDate 2013
url 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
geographic Pacific
geographic_facet Pacific
genre Crassostrea gigas
Pacific oyster
genre_facet Crassostrea gigas
Pacific oyster
op_relation 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. Bradley J (Editor), Heljanko K (Editor), Knottenbelt W (Editor) & Thomas N (Editor) PASM'12: Sixth International Workshop on Practical Applications of Stochastic Modelling, Imperial College London, UK, 17.09.2012-17.09.2012. Electronic Notes in Theoretical Computer Science, 296, pp. 211-228. https://doi.org/10.1016/j.entcs.2013.07.014
http://homepages.cs.ncl.ac.uk/nigel.thomas/PASM12.htm#publication
http://hdl.handle.net/1893/16641
doi:10.1016/j.entcs.2013.07.014
WOS:000216919300014
2-s2.0-84883387223
687726
http://dspace.stir.ac.uk/bitstream/1893/16641/1/PEPA%27d%20oysters.pdf
op_rights This article is open-access. Open access publishing allows free access to and distribution of published articles where the author retains copyright of their work by employing a Creative Commons attribution licence. Proper attribution of authorship and correct citation details should be given.
http://creativecommons.org/licenses/by-nc-nd/4.0/
op_rightsnorm CC-BY
CC-BY-NC-ND
op_doi https://doi.org/10.1016/j.entcs.2013.07.014
container_title Electronic Notes in Theoretical Computer Science
container_volume 296
container_start_page 211
op_container_end_page 228
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