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Journal Article

Cacatoo: building, exploring, and sharing spatiallystructured models of biological systems


van Dijk,  Bram
Department Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Max Planck Society;

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van Dijk, B. (2022). Cacatoo: building, exploring, and sharing spatiallystructured models of biological systems. The Journal of Open Source Software, 7(70): 3948. doi:10.21105/joss.03948.

Cite as: https://hdl.handle.net/21.11116/0000-0009-FB6B-5
In the field of ecology and evolution, a treasure trove of data has revealed the importance ofspatial structure and biogeography. Despite these rich data sets, our conceptual understand-ing of how spatial structure shapes biodiversity, pathogenicity, and microbial pangenomesis lagging behind. For example, we only have a limited understanding of how interactionsat the microscale (molecular machinery, bacteriophages, metabolism) scale up to define eco-evolutionary dynamics of microbial communities (Rainey & Quistad, 2020) and metaorganisms(Jaspers et al., 2019). To develop our intuition on these systems, I argue we need to embracemultiple levels and structural complexity in our models.Cacatoois a toolbox developed tomake it easy to design, explore, and share simulations of such systems. Simulations can beinteractively explored from a web browser, allowing the user to change parameters and observegraphs in real-time.Cacatoois designed to be both easy-to-use and extendable, making itsuitable for beginners and experts alike. Because it requires no installation and works on prac-tically every computer, it is also ideal for teaching purposes and student projects. In summary,Cacatooprovides opportunities for everyone to get involved in spatially structured modelling