Designing microbial communities using genome-scale metabolic models.
Can be easily installed using pip:
pip install designmc
DesignMC is a tool for designing synthetic microbial communities with a desired phenotypic trait (i.e. design target) using genome-scale metabolic models. The minimum required input is a list of single-species models, one design target (secreted metabolite), and a definition of the growth medium:
designmc models/*.xml -t trp__L -m M9 -d mediadb.tsv
Please note that this tool is still under development. It currently only supports models using BiGG notation, such as those created with CarveMe. The only design strategy currently available is random sampling.
You can control the maximum number of species per community (example:
-s 5 or --species 5) and the maximum number of combinations to
simulate (-n 100 or --iters 100).
For more options and details please check the help menu:
designmc -h
Daniel Machado, European Molecular Biology Laboratory (EMBL), 2020