the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 05 Aug 2025
BORIS-2 – a benthic ecosystem model based on allometry
Abstract. We present a model describing the population dynamics of benthic biota, feeding from a common resource that is supplied by a flux of sinking organic carbon arriving on the seafloor. By using allometric relationships for the physiological processes of growth, mortality and respiration, and for food limitation, the model represents the population dynamics of organisms ranging in size from bacteria (10-14 g wet weight C) to large metazoans (103 gwwt C). The effect of temperature on physiological rates is also included. The only forcing information required is the ambient temperature and the rate of supply of sinking organic carbon. The model can be used for, and tuned to, specific locations. However, a parameter set is provided that is generally applicable. The ability of the model to simultaneously reproduce biomass size distributions at five contrasting sites is demonstrated for this parameter set. Other examples of use are also shown, using the model to explore global patterns of benthic biomass, and responding to a change in food supply.
Competing interests: At least one of the (co-)authors is a member of the editorial board of Geoscientific Model Development.
Publisher's note: Copernicus Publications remains neutral with regard to jurisdictional claims made in the text, published maps, institutional affiliations, or any other geographical representation in this paper. While Copernicus Publications makes every effort to include appropriate place names, the final responsibility lies with the authors. Views expressed in the text are those of the authors and do not necessarily reflect the views of the publisher.- Preprint
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Status: open (until 03 Oct 2025)
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CEC1: 'Comment on egusphere-2025-2180', Juan Antonio Añel, 08 Aug 2025
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CC1: 'Reply on CEC1', Andrew Yool, 08 Aug 2025
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Dear Juan,
Thank you for your assessment of our repository. This is just to confirm that it does contain the model code, both for running in steady state (via steady_state.m) and dynamic (via benthic_dydt.m) modes. The repository also contains the scripts necessary for producing the figures that appear in the manuscript, and our Supplement includes a User Manual for using the scripts archived in the Zenodo record. If you think that any of these materials are insufficiently clear, please let us know and we will amend them when the manuscript is revised. We hope this is sufficient clarification for our manuscript's Discussion to proceed.
With best regards,
Andrew Yool.
Citation: https://doi.org/10.5194/egusphere-2025-2180-CC1 -
CEC2: 'Reply on CC1', Juan Antonio Añel, 08 Aug 2025
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Dear authors,
Thanks for the quick clarification. Our doubt was caused by the fact that routines included look quite basic, only showing a few parameters and lines of code. Could it be that you have included relevant information in the binary files (.mat) which we can not read? It would be good if you could avoid sharing information as binary files that only can be read using the M language interpreter. If you can, please, do it.
Juan A. Añel
Geosci. Model Dev. Executive Editor
Citation: https://doi.org/10.5194/egusphere-2025-2180-CEC2 -
CC2: 'Reply on CEC2', Andrew Yool, 08 Aug 2025
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Dear Juan,
As an allometric model with only a few process terms, BORIS is deceptively simple, so its codebase is quite brief. Running it does not require the *.mat files directly - these provide geographical boundary conditions / forcing. As the model is essentially non-spatial, this forcing information is ordinarily provided via its parameter list. However, this sort of additional geographical information allows BORIS to be run for arbitrary spatial locations, or to be run across the globe systematically, as can be see in Figure 4. I hope this answers your question.
With best regards,
Andrew Yool.
Co-author.
Citation: https://doi.org/10.5194/egusphere-2025-2180-CC2
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CC2: 'Reply on CEC2', Andrew Yool, 08 Aug 2025
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CEC2: 'Reply on CC1', Juan Antonio Añel, 08 Aug 2025
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AC1: 'Reply on CEC1', Adrian Martin, 18 Aug 2025
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I am very sorry for my delay in replying but I am only just back from leave.
With thanks to him for doing so in my absence, I hope the response by co-author Andrew Yool has addressed your concerns.
By way of summary, we have provided all code necessary to run the model and all data files needed to reproduce all figures in the manuscript. The code has been fully listed and described on the associated Zenodo page and there is additionally a User Guide included as Supplementary Material to the manuscript.
The model may appear simple but this is largely because the use of allometry allows considerable computational efficiency when modelling the dynamics of organisms spanning a very large range of sizes. This advantage offered by the allometric approach is a significant factor in why we thought GMD the ideal journal to publish in. The model simultaneously and explicitly simulates the dynamics of 59 size groups of organisms as well as the food supply supporting them.
If you need any further information please don't hesitate to ask.
Citation: https://doi.org/10.5194/egusphere-2025-2180-AC1
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CC1: 'Reply on CEC1', Andrew Yool, 08 Aug 2025
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Dear authors,
After checking your manuscript, we have great doubts about its compliance with the Code and Data policy of our journal.
https://www.geoscientific-model-development.net/policies/code_and_data_policy.html
In the Zenodo repository that you cite, a few routines are shared (namely four M language scripts), which do not seem to be the full BORIS-2 model that you present in your manuscript.
Our policy is clear regarding the fact that all the code and data necessary to replicate the work presented in a manuscript must be public and without access restrictions before the submission of a manuscript to our journal. Therefore, please clarify if the current code in the Zenodo repository that you have shared is all the BORIS-2 code. If it is not the case, please, in a prompt manner publish the BORIS-2 code in an acceptable repository from the ones listed in our policy, and reply to this comment with the information for it: links and permanent handler (e.g. DOI).
I note that in lack of compliance with our policy we will have to reject your manuscript for publication.
Juan A. Añel
Geosci. Model Dev. Executive Editor