Published March 31, 2026
| Version v2
Software
Open
Matlab code associated with the BORIS-2 benthic ecosystem model
Contributors
-
1.
National Oceanography Centre
Description
This code is linked to the manuscript:
BORIS-2 – a benthic ecosystem model based on allometry
Adrian P. Martin, Anieke Brombacher, Noelie Benoist, Brian J. Bett, Jennifer M. Durden, Sophy Oliver, Andrew Yool
Submitted to Geoscientific Model Development - egusphere-2025-2180
Contact: adrian.martin@noc.ac.uk
Code is provided to generate the figures in the manuscript, but which is also of more general use.
All code is in Matlab. It was developed, tested and run in version 25.1.0.2973910 (R2025a) Update 1.
Overview:
BORIS-2 is 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 (10^3 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 model can simultaneously reproduce biomass size distributions at five contrasting sites using this parameter set. This model has an analytic steady state solution and can also be run dynamically.
The model has been configured using data from 5 contrasting sites. Details can be found in the manuscript and locations are shown by Fig3.m. In the order in which they are used/referred to in the code, these sites are:
1. Clarion Clipperton Zone (CCZ)
2. Fladden Ground (FG)
3. Faroe Shetland Channel (FSC)
4. Oman Margin (OM)
5. Porcupine Abyssal Plain (PAP)
Code description:
params.m
- Sets parameters used in the BORIS-2 model - called by both dynamic and steady state versions
rates.m
- Uses information from params.m and location temperature to set physiological rates (maximum growth, respiration and mortality) and interference
- Other routines called:
param.s
siteinfo.m
- Sets up information on the 5 sites used in the manuscript
- Information is:
site location (latitude and longitude)
seafloor temperature
temperature effect on rates
steady_state.m
- Function to calculate steady state solution given input of temperature and POC flux
- Equations for steady state are given in manuscript
- Other routines called:
param.s
rates.m
benthic_dydt.m
- Function to calculate rate of change of biomass and detritus with time for use in dynamical version of model
- Equations are given in manuscript
- Other routines called:
None directly but requires global variables for fluxes, time and rates to have been set up - see Fig7.m for example
Fig2.m
- Creates Figure 2 for the manuscript: plots showing how the growth limitation function f(R,B) varies with both R and B
- Creates Figure 3 for the manuscript: a fit of a power law to observations of biomass from 5 contrasting sites
- Other routines called:
param.m
- Data used:
BiomassData.zip
Fig4.m
- Creates Figure 4 for the manuscript: a set of diagnostics for assessing the performance of the model
- Other routines called:
param.s (by calling Fig3.m)
rates.m
Fig3.m
- Data used:
BiomassData.zip (by calling Fig3.m)
Fig5.m
- Creates Figure 5 for the manuscript: a set of sensitivity analyses for metrics shown in Figure 4
- Other routines called:
param.s
rates.m
siteinfo.m
- Creates Figure 6 for the manuscript: showing global distribution of benthic biomass based on temperature and POC flux data
- Uses batlow color map, part of Scientific Color Maps (c) 2023, Fabio Crameri - see notes below
- Other routines called: param.s
rates.m (by calling steady_state.m)
steady_state.m
- Data used:
WOAbott,mat
fluxglobdat,mat
- Also uses:
Scientific Color Maps
- Creates Figure 7 for the manuscript: showing response of ecosystem to a doubling of POC flux
- This code is easily modified to explore other situations with time-varing POC flux and temperature
- Other routines called:
param.s
rates.m
steady_state.m
benthic_dydt.m
Data:
WOAbott.mat
- Seafloor latitude, longitude, depth and temperature data extracted from the World Ocean Atlas - Reagan et al. (2024)
- Used by Fig6.m
fluxglobdat.mat
- POC fluxes calculated using Lutz. et al. (2007) algorithm for same latitude, longitude grid and depths as WOAbott.mat
- Used by Fig6.m
BiomassData.zip
- Compressed folder with biomass observations from the 5 sites used in the manuscript
CCZ_biomass
FG_biomass
FSC_biomass
OM_biomass
PAP_biomass
- Information on sites and how data were generated can be found in the manuscript
- Used by Fig3.m (and indirectly by Fig4.m by running Fig3.m)
Scientific Color Maps (c) 2023, Fabio Crameri
Fig6.m makes use of the batlow color map which is part of this suite of color maps created by Fabio Crameri.
They are designed to optimise viewing for as wide a range of people as possible.
The Scientific colour maps are licensed under a MIT License.
More information can be found here: https://www.fabiocrameri.ch/colourmaps/
Files
BiomassData.zip
Files
(71.3 MB)
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Additional details
Funding
Dates
- Created
-
2026-03-31Version of code corresponding to manuscript submitted to GMD - egusphere-2025-2180
Software
- Programming language
- MATLAB
References
- Reagan, J. R., Boyer, T. P., García, H., Locarnini, R. A., Baranova, O. K., Bouchard, C., Cross, S. L., Mishonov, A. V., Paver, C. R., Seidov, D., Wang, Z., Dukhovskoy, D.: World Ocean Atlas 2023. NOAA National Centers for Environmental Information. Dataset: NCEI Accession 0270533, 2024.
- Lutz, M. J., Caldeira, K., Dunbar, R.B., and Behrenfeld, M.J.: Seasonal rhythms of net primary production and particulate organic carbon flux to depth describe the efficiency of biological pump in the global ocean, J. Geophys. Res., 112, C10011, doi:10.1029/2006JC003706, 2007