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An online tool to easily run stock assessment models, using SS3 and SWO as an example ArchiMer
Nieblas, Anne-elise; Bonhommeau, Sylvain; Imzilen, Taha; Fu, Dan; Fiorellato, Fabio; Barde, Julien.
Tipo: Text
Ano: 2017 URL: http://archimer.ifremer.fr/doc/00403/51439/52008.pdf
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Collecting information on the pelagic phase of marine turtles from at-sea observations: The case of purse seine fisheries in the Indian Ocean ArchiMer
Chassot, Emmanuel; Sabarros, Philippe; Maufroy, A; Ruiz, J; Ramos, Ml; Barreau, E; Barde, Julien.
Observations of turtles in the open-ocean are essential to complement the information collected at nesting sites and rookeries, especially during the ‘lost years’ of their surface-pelagic juvenile phase. We used a large dataset of observations at sea collected onboard Seychelles, Spanish and French purse seiners over the period 2003-2019 to describe the occurrence of five species of turtles in the Western Indian Ocean: green ( Chelonia mydas ), loggerhead ( Caretta caretta ), leatherback ( Dermochelys coriacea ), Olive ridley ( Lepidochelys olivacea ) and hawksbill ( Eretmochelys imbricata ). A total of 895 turtles were recorded by human observers, 487 turtles after having been caught in the purse seine and hauled onboard the vessels and 408 turtles...
Tipo: Text
Ano: 2019 URL: https://archimer.ifremer.fr/doc/00599/71131/69446.pdf
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Eating up the world's food web and the human trophic level ArchiMer
Bonhommeau, Sylvain; Dubroca, Laurent; Le Pape, Olivier; Barde, Julien; Kaplan, David; Chassot, Emmanuel; Nieblas, Anne-elise.
Trophic levels are critical for synthesizing species' diets, depicting energy pathways, understanding food web dynamics and ecosystem functioning, and monitoring ecosystem health. Specifically, trophic levels describe the position of species in a food web, from primary producers to apex predators (range, 1-5). Small differences in trophic level can reflect large differences in diet. Although trophic levels are among the most basic information collected for animals in ecosystems, a human trophic level (HTL) has never been defined. Here, we find a global HTL of 2.21, i.e., the trophic level of anchoveta. This value has increased with time, consistent with the global trend toward diets higher in meat. National HTLs ranging between 2.04 and 2.57 reflect a...
Tipo: Text Palavras-chave: Human ecology; Nutrition transition; Trophic ecology.
Ano: 2013 URL: http://archimer.ifremer.fr/doc/00171/28190/26609.pdf
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Online collaborative environment to run Stock Assessment work ow: an option for IOTC? ArchiMer
Imzilen, Taha; Bonhommeau, Sylvain; Rouyer, Tristan; Kell, Laurence T; Chassot, Emmanuel; Barde, Julien.
In this note, we present an approach which has been recently used to execute online the set of codes used for eastern blue_n tuna (BFT-E) stock assessment at ICCAT. We aim at discussing the possible interest of the approach to the IOTC Community for focusing on Indian ocean tuna and tuna-like stocks and running other assesment models such as Stock Synthesis 3 (SS3). In 2014, ICCAT BFT-E working group has been able to execute thousands of model runs by using parallelization of R and Fortran codes on a supercomputer. This approach has a lot of scienti_c bene_ts, in particular for better including the multiple sources of uncertainty in assessment results and associated scienti_c advice. However, very few participants would be able to reproduce it without...
Tipo: Text
Ano: 2016 URL: http://archimer.ifremer.fr/doc/00360/47135/47084.pdf
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Online collaborative environment to run the eastern bluefin tuna stock assessment workflow ArchiMer
Imzilen, Taha; Bonhommeau, Sylvain; Rouyer, Tristan; Kell, Laurence T; Barde, Julien.
In this note, we describe an approach which makes possible to execute online the set of codes used for eastern bluefin tuna (BFT-E) stock assess-ment at ICCAT. In 2014, ICCAT BFT-E working group has been able to execute thousands of model runs by using parallelization of R and Fortran codes on a supercomputer. This new approach has a lot of scientific benefits, but very few participants would be able to reproduce it without specific skills. Since november 2015, the H2020 BlueBridge project is funding an engineer to set up a WebSite (or VRE for Virtual Research Environment) where users will be able to parametrize and execute various steps of the BFT-E stock assessment workflow. By repackaging codes provided by ICCAT BFT-E working group the same codes are...
Tipo: Text Palavras-chave: Bluefin tuna; Scientific cloud; Stock assessment; Grid computing; Online processing.
Ano: 2017 URL: http://archimer.ifremer.fr/doc/00403/51471/52042.pdf
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