Repository for updated and standardized model of Mycobacterium tuberculosis H37Rv, iEK1011 (and the BiGGs quality iEK1008 model)
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.ipynb_checkpoints
Dataframes
TB_previous_models
escher_maps
iEK1008_BiGGs_reconstructions
iEK1011_reconstructions
Figure3_revised.png
README.md
TB_recon_data.xlsx
amr_gene_dic.json
gurobi.log
reproducible_iEK1008_workflow.ipynb
reproducible_iEK1011_workflow.ipynb
sMtb_conversion_BiGGs.json
sMtb_mapped_model.json
supplementary_tables.docx

README.md

iEK1011

Repository for the unified, standardized, and updated model of Mycobacterium tuberculosis H37Rv, iEK1011 and the BiGGs quality iEK1008 model), described in

Erol S. Kavvas, Y. Seif, JT. Yurkovich, C. Norsigian, S. Poudel, WW. Greenwald, S. Ghatak, BO. Palsson, JM. Monk. Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions. BMC Systems Biology 2018 12:25_

alt text

Installation

git clone https://github.com/erolkavvas/iEK1011_materials.git

Key scripts

  • reproducible_iEK1011_workflow.ipynb
  • reproducible_iEK1008_workflow.ipynb

Location of models initialized with different media conditions

  • iEK1011_reconstructions
  • iEK1008_BiGGs_reconstructions