ECOTRAN vertically-resolved end-to-end ecosystem model code for the Gulf of Mexico

This dataset contains model code for the vertically-resolved ECOTRAN end-to-end ecosystem model for the oceanic Gulf of Mexico. The model quantifies rates of energy and biomass transfer between the epipelagic and deep pelagic ecosystems that occur via trophic interactions and particle sinking. The model also uses simulations to estimate the consequences to ecosystem dynamics from perturbations to trophic linkages and to particle fluxes. The model code is written and executed in Matlab (https://www.mathworks.com). The model code, supporting functions, and explanatory documentation are also archived at the NSF Biological and Chemical Oceanography Data Management Office project 544746 (https://www.bco-dmo.org/project/544746). The model consists of two parts. The first is the structure and code of the model. ECOTRAN quantifies biomass transfer between multiple functional groups across all trophic levels representing planktonic, pelagic and benthic communities, and fisheries. As an end-to-end ecosystem model, it also accounts for detritus and nutrient cycling. The model is spatially resolved and considers the physical fluxes of nutrients, plankton, and detritus between sub-regions. The oceanic Gulf of Mexico will be vertically resolved into three sub-regions: upper-pelagic/euphotic, mesopelagic, and bathypelagic/benthic. The basic structure of ECOTRAN is described in two peer-reviewed publications, Steele and Ruzicka (2011) and Ruzicka et al., (2016). The second part of the model is the parameterization describing the physiological rates, trophic linkages, and physical linkages within and between sub-regions. This model shall use as its foundation for mid-and upper trophic levels, the parameter set of the northern coastal Gulf of Mexico ECOPATH food web model developed and documented by Robinson et al., (2015). Parameterization of deep-pelagic nekton and micronekton community structure and physiologies are to be obtained from ocean surveys, stomach content, stable isotope, and detritus flux data sources listed in the GRIIDC data archive for GoMRI RFP VI project “Deep-pelagic plankton: communities of the northern Gulf of Mexico: trophic ecology, assemblage dynamics, and connectivity with the upper ocean.” The dataset includes visual basic code to provide the ECOPATH mass-balanced budget. Matlab scripts provide the Ecotran model, the ability to construct Monte Carlo models, and ecosystem perturbation evaluations. The code and process of running the model are well-documented in the included manual.