BACILLUSme

BACILLUSme contains all the information and building scripts required to construct a ME-model for B. subtilis, iJT964-ME using COBRAme. See the COBRAme github and documentation for further instructions on how to build and solve ME-models. This package is based on and is homologous to ECOLIme. Minor changes were necessary for COBRAme to function with this organism, so find the modified COBRAme we used for iJT964-ME here.

If you are using BACILLUSme or iJT964-ME, please cite doi:10.1038/s41540-022-00259-0.

Installation

1. clone the repository
2. run python setup.py develop --user
3. Run build_me_model.ipynb to construct and save iJT964-ME.
4. The saved model can be solved using solve_demo.ipynb