the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Parameterization and tuning of the Bay of Biscay Atlantis model v1
Cecilie Hansen
Xavier Corrales
Iñaki Quincoces
Izaskun Preciado
Eider Andonegi
Abstract. This paper describes the parameterization and calibration of an end-to-end Atlantis model for the Bay of Biscay, characterising spatially the structure and functioning of the ecosystem. The Bay of Biscay is considered rich in terms of ecological diversity and different oceanographic events such as coastal upwelling, coastal run-off and river plumes, and seasonal currents, take place in the area. These features, in addition to the different pressures caused by human activities and management criteria, demand for concurrent modelling of all the characteristics of the Bay of Biscay ecosystem in order to improve our understanding of the system and its functioning. The modelled area is 145 970 km2 and was divided into 36 spatial polygons, each with multiple vertical layers. The model was composed by 54 functional groups, ranging from primary producers to top predators. Our results highlighted the importance of lower trophic levels to the pelagic system and how the trophic interactions among phytoplankton and zooplankton groups impact the structure of the ecosystem. The results also demonstrate the importance of having accurate and precise data for biological processes and showed the need of further study in the age-specific data such as biomass and weight distribution per age and diet interactions between juvenile and adult fish stages. Overall, the Bay of Biscay Atlantis model has been shown to be a tool that has the potential to improve our understanding of the spatial functioning of the Bay of Biscay ecosystem that will help establishing management measures of human activities.
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Ane Lopez de Gamiz-Zearra et al.
Status: open (until 31 Dec 2023)
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CEC1: 'Comment on egusphere-2023-1368', Juan Antonio Añel, 11 Oct 2023
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Dear authors,
Unfortunately, after checking your manuscript, it has come to our attention that it does not comply with our "Code and Data Policy".
https://www.geoscientific-model-development.net/policies/code_and_data_policy.htmlFirst, independently, if you do have or do not have the right to publish the code you use in your work, it is necessary that you archive it permanently. Therefore, please, upload the Atlantis code to a Zenodo private repository, and reply to this comment with the DOI and link to access it.
Also, in your manuscript, you state, "This information is required to filter out fake registrations (bots), and to plan future model development and user support. For further details see https ://github.com/ Atlantis‐Ecosystem‐Model/
Atlantis_example_and_instructions." The statement on the need for information is irrelevant here and even misleading, as the reasons that you mention are debatable. Therefore, in potential future reviewed versions of your manuscript, please, remove it. Regarding the "further details", you have stored them in GitHub. First, the link is not working, so it is not possible to access such information. Second, GitHub is not a suitable repository for scientific publication, our policy makes it clear. Moreover, GitHub itself instructs authors to use other alternatives for long-term archival and publishing, such as Zenodo. Therefore, please, publish your "further details" in one of the appropriate repositories, and reply to this comment with the relevant information (link and DOI) as soon as possible, as it should be available before the Discussions stage.Juan A. Añel
Geosci. Model Dev. Executive Editor
Citation: https://doi.org/10.5194/egusphere-2023-1368-CEC1 -
AC1: 'Reply on CEC1', Ane Lopez de Gamiz Zearra, 01 Nov 2023
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Dear Juan,
Sorry for our late reply to your comment. The model developer (affiliated with CSIRO, Australia) suggests that the reviewers registert, and that way can get access to the code. The registration is necessary to protect government IP to meet export laws in Australia, and none of the authors of the manuscript will have access to the overview of registered users. If you accept this, we'll create a repositoty to share the remaining code and files used in the development of the manuscript.
Ane
Citation: https://doi.org/10.5194/egusphere-2023-1368-AC1 -
CEC2: 'Reply on AC1', Juan Antonio Añel, 01 Nov 2023
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Dear authors,
First, thanks for your reply.
While we can understand that some researchers are not allowed to share the code because of legal reasons imposed by their employers, it is not clear to me what law or regulation forbids you or the developers from storing the model in a long-term repository such as the ones offered by Zenodo (private or not). Therefore, we need more detailed information on the regulations that forbid the authors to share it to judge if we can accept an exception in this case.
I understand that in this work, all the authors are simply users, and none of you is involved in the development of the model used. If this is the case, this would be an extra possibility to clear your manuscript in compliance with our Code and Data Policy, as you would not have a way to influence the decision on the license or sharing of the model. However, we need clarification on this too.
Regards,
Juan A. Añel
Geosci. Model Dev. Executive Editor
Citation: https://doi.org/10.5194/egusphere-2023-1368-CEC2 -
AC2: 'Reply on CEC2', Ane Lopez de Gamiz Zearra, 03 Nov 2023
reply
Dear Juan,
The Atlantis code was developed by employees of the Australian government and so automatically falls under both Australian export laws and Crown Copyright. This means that while the code can be distributed royalty free from the CSIRO repository it cannot be posted to a public repository long or short term. Anyone accessing the code has to be registered to comply with this ruling by CSIRO’s legal department. The developers are very happy to register applicants or to provide the manual to any interested users - that is able to be shared widely and is already publcially accessible with full documentation of equations used.
We, the authors, are simply users of the model, so none of us is involved in the development or/and improvement of the model used.
Ane
Citation: https://doi.org/10.5194/egusphere-2023-1368-AC2
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AC2: 'Reply on CEC2', Ane Lopez de Gamiz Zearra, 03 Nov 2023
reply
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CEC3: 'Reply on AC1', Juan Antonio Añel, 01 Nov 2023
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Dear authors,
A clarification on the other comment that I have posted replying to you. In the first paragraph, when I refer to "the authors", I mean the authors of the model, not the authors of the manuscript, as in the second paragraph.
Juan A. Añel
Geosci. Model Dev. Executive Editor
Citation: https://doi.org/10.5194/egusphere-2023-1368-CEC3
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CEC2: 'Reply on AC1', Juan Antonio Añel, 01 Nov 2023
reply
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AC1: 'Reply on CEC1', Ane Lopez de Gamiz Zearra, 01 Nov 2023
reply
Ane Lopez de Gamiz-Zearra et al.
Ane Lopez de Gamiz-Zearra et al.
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