An agent-based model of the gut microbial community and its repsonse to diet.
A comprehensive explanation of how the model works can be found in this PDF file.
I launch GutSim from Bash (I use a Mac).
You can use the launch.py script.
There are several command line options that can be used to supply
- the location of the parameters.xml file to use,
- the location to which data should be written,
- the random number seed to use.
python launch.py -m <mouse ID here> -p parameters-replicates.xml -d results/example_output_directory -seed 999
There are more options too.
You will find a lot of this documented at the bottom of the main method at the bottom of gutsim/experiment.py.
GutSim was first introduced in:
Holmes, A. J., Chew, Y. V., Colakoglu, F., Cliff, J. B., Klaassens, E., Read, M. N., … Simpson, S. J. (2017). Diet-Microbiome Interactions in Health Are Controlled by Intestinal Nitrogen Source Constraints. Cell Metabolism, 25, 140–151. https://doi.org/10.1016/j.cmet.2016.10.021
We are currently working on a follow up paper that focused on the gut microbiome's response to periodic fasting and prebiotics.