Post, Benjamin ORCID:, Acevedo-Trejos, Esteban, Barton, Andrew D. and Merico, Agostino ORCID: (2024) The XSO framework (v0.1) and Phydra library (v0.1) for a flexible, reproducible, and integrated plankton community modeling environment in Python. Geoscientific Model Development, 17 (3). pp. 1175-1195. DOI

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Plankton community modeling is a critical tool for understanding the processes that shape marine ecosystems and their impacts on global biogeochemical cycles. These models can be of variable ecological, physiological, and physical complexity. Many published models are either not publicly available or implemented in static and inflexible code, thus hampering adoption, collaboration, and reproducibility of results. Here we present Phydra, an open-source library for plankton community modeling, and Xarray-simlab-ODE (XSO), a modular framework for efficient, flexible, and reproducible model development based on ordinary differential equations. Both tools are written in Python. Phydra provides pre-built models and model components that can be modified and assembled to develop plankton community models of various levels of ecological complexity. The components can be created, adapted, and modified using standard variable types provided by the XSO framework. XSO is embedded in the Python scientific ecosystem and is integrated with tools for data analysis and visualization. To demonstrate the range of applicability and how Phydra and XSO can be used to develop and execute models, we present three applications: (1) a highly simplified nutrient–phytoplankton (NP) model in a chemostat setting, (2) a nutrient–phytoplankton–zooplankton–detritus (NPZD) model in a zero-dimensional pelagic ocean setting, and (3) a size-structured plankton community model that resolves 50 phytoplankton and 50 zooplankton size classes with functional traits determined by allometric relationships. The applications presented here are available as interactive Jupyter notebooks and can be used by the scientific community to build, modify, and run plankton community models based on differential equations for a diverse range of scientific pursuits.

Document Type: Article
Programme Area: PA2
Research affiliation: Integrated Modelling > Systems Ecology
Refereed: Yes
Open Access Journal?: Yes
ISSN: 1991-9603
Date Deposited: 23 Feb 2024 09:06
Last Modified: 26 Mar 2024 13:31

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