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

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.

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10.21105.joss.03948.pdf (Publisher version), 297KB
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van Dijk, Bram1, Author           
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1Department Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_2421699              

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 Abstract: 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

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Language(s): eng - English
 Dates: 2021-11-092022-02-052022
 Publication Status: Published in print
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 Identifiers: DOI: 10.21105/joss.03948
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Title: The Journal of Open Source Software
  Abbreviation : J. Open Source Softw.
Source Genre: Journal
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Pages: - Volume / Issue: 7 (70) Sequence Number: 3948 Start / End Page: - Identifier: ISSN: 2475-9066
CoNE: https://pure.mpg.de/cone/journals/resource/2475-9066