As someone who frequently programs (relatively) complex biological models, I frequently rely on direct visual feedback. Visualisations can not only help to quickly see the results of my program, but also allows the debugging of strange behaviour. However, such visualisation can really slow things down, and I have therefore always stuck with programming in C with the lightning-fast X11 library. However, both C and X11 are as dated as they are hard to work with. Moreover, every operating system needs a different compiler for the C code, while support for X11-library is waning. Rarely does a piece of C-code simply run “out of the box”.
As someone who works primarily with models in which individuals have spatial coordinates, I have struggled a lot with visualising these systems. If you are using similar models, or biological data sets that have a similar structure of datapoints with x- and y-coordinates, here’s a few things I’ve picked up to make them prettier.
But first, let’s start at step 0, and read some data…
After years of development, Virtual Microbes are finally starting to give us new biological insights. The first piece of work is now peer-reviewed and published, but if you have little time, see a video abstract of what we did right here:
I am a computational biologist studying microbial ecology and evolution with a key focus on horizontal gene transfer (HGT). This website is primarily dedicated to the science, the programming, and the visualisation of cool biological systems. However, it may also contain whatever else I feel like sharing.