Data and tools necessary to construct iJL1678b-ME, a genome-scale model of E. coli K-12 MG1655 metabolism and expression
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ecolime
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README.md
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README.md

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