Articles | Volume 17, issue 3
Model description paper
13 Feb 2024
Model description paper |  | 13 Feb 2024

The XSO framework (v0.1) and Phydra library (v0.1) for a flexible, reproducible, and integrated plankton community modeling environment in Python

Benjamin Post, Esteban Acevedo-Trejos, Andrew D. Barton, and Agostino Merico

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Cited articles

Acevedo-Trejos, E., Brandt, G., Bruggeman, J., and Merico, A.: Mechanisms shaping size structure and functional diversity of phytoplankton communities in the ocean, Sci. Rep., 5, 8918,, 2015. a
Acevedo-Trejos, E., Brandt, G., Smith, S. L., and Merico, A.: PhytoSFDM version 1.0.0: Phytoplankton Size and Functional Diversity Model, Geosci. Model Dev., 9, 4071–4085,, 2016. a
Anderson, T. R.: A spectrally averaged model of light penetration and photosynthesis, Limnology and Oceanography, 38, 1403–1419,, 1993. a, b, c
Anderson, T. R.: Plankton functional type modelling: Running before we can walk?, J. Plankton Res., 27, 1073–1081,, 2005. a
Anderson, T. R., Gentleman, W. C., and Yool, A.: EMPOWER-1.0: an Efficient Model of Planktonic ecOsystems WrittEn in R, Geosci. Model Dev., 8, 2231–2262,, 2015. a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s
Short summary
Creating computational models of how phytoplankton grows in the ocean is a technical challenge. We developed a new tool set (Xarray-simlab-ODE) for building such models using the programming language Python. We demonstrate the tool set in a library of plankton models (Phydra). Our goal was to allow scientists to develop models quickly, while also allowing the model structures to be changed easily. This allows us to test many different structures of our models to find the most appropriate one.