Cacatoo

Cacatoo is a toolbox for modelling and exploration of spatially structured simulations. Because it is written in 100% javascript it requires no installation and works on any machine, making building, sharing, and exploring your model easier than it ever was! With a web-based interface that is ideal for students to learn how to program, and a NodeJS-mode which allows one to rapidly run simulations directly from the command line, it is suited for beginners and advanced programmers alike!


Cacatoo is roughly based on a tried-and-true c-library called Cash (RJ de Boer & AD Staritsk) but is much easier to work with. It also comes with a few new features, such as the ability to integrate ODEs on a grid with diffusion (i.e. a numeric approximation of a PDE). Cacatoo is available on Github, and more documentation and tutorials are also available. If you want to see an example model in action, click on the button below!

Xenoseq

Xenoseq is a simple bioinformatic pipeline to find sequences that appear to be newly introduced into a community. Xenoseq wraps read trimming (fastp), assembly (megahit), read mapping (BWA), read filtering (samtools), and local alignment (blast), to detect putative evidence of horizontal transfer between communities. It also generates output for the estimated abundance of these “xenotypic sequences” across all samples.

Virtual Microbes

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Microbial evolution with artificial chemistry

Virtual Microbes is a computer simulation model to study the eco-evolutionary dynamics of microbes (Thomas Cuypers, 2018). Virtual Microbes is unsupervised, meaning that it targets to combine relevant biological structures (genes, genomes, metabolism, mutations, ecology, etc.) without a preconceived notion of “fitness”, which is instead an emergent phenomenon. By not explicitly defining what the model should do, it allows for a serendipitous approach to study microbial evolution:

  • How do complex cross-feeding communities form?

  • What happens when a complex microbe “wild type” is transferred to lab-like conditions?

  • What is the influence of horizontal gene transfer (HGT) on the productivity and diversity of a microbial community?

Find Virtual Microbes on bitbucket

Cash 2.1

("the old Cacatoo")
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What is Cash2.1?

Cash2.1 is an easy-to-use library to make a program simulating Cellular Automata (CAs). It is based on Cash1.0 (RJ de Boer & AD Staritsk) and was further developed by Nobuto Takeuchi (2s) and Bram van Dijk (2.1), and used in the course Computational Biology given by Paulien Hogeweg at Utrecht University.

Downloading and installation

The software is freely* available for download here. A complete user manual is available for usage and installation.

Future programming plans

  • A biophysics simulation of growing, rod-shaped cells to study the ecology of “shoving”

  • VirtualMicrobes 2.0, improving Virtual Microbes based on what we’ve learned from Virtual Microbes

  • Something secret, with one dimension more than my usual stuff :)

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