ECOLIme

ECOLIme contains all the information and building scripts required to construct a ME-model for E. coli K-12 MG1655, iJL1678b-ME using COBRAme. See the COBRAme github and documentation for further instructions on how to build and solve ME-models.

Note: The current version of iJL1678b-ME is provided prior to peer-reviewed publication. The model may be edited and updated until it is finalized for publication.

Installation

1. clone the repository
2. run python setup.py develop --user
3. Run build_me_model.py or build_me_model.ipynb to construct and save iJL1678b-ME
4. The saved model can be solved using solve_demo.ipynb

codon table source: http://openwetware.org/wiki/Escherichia_coli/Codon_usage