DeepMGR

• Note: This source code was developed in Linux, and has been tested in Ubuntu 16.04 with Python 3.9

• Major dependency: rdkit

Source

1. Clone the repository

   git clone https://bitbucket.org/kaistsystemsbiology/DeepMGR.git
   

2. Create and activate a conda environment

   conda env create -f environment.yml
   conda activate deepmgr
   

Example

• Run deepMGR with input files in ‘./input’.

  python run_deepmgr.py -i -s MG1655
  

• Run deepMGR without input files in ‘./input’.

  python run_deepmgr.py -b oxygen -c [Glucose,2] [Na2HPO4,12.8] [KH2PO4,3] [NaCl,0.5] [NH4Cl,1]
  [MgSO4,0.24] [CaCl2,0.0111] -s BW25113 -g b0001
  

• For more information:

  python run_deepmgr.py -h
  

Publication - Mun Su Kwon, Joshua Julio Adidjaja and Hyun Uk Kim. Predicting the effects of cultivation condition on gene expression levels in Escherichia coli by using deep learning.

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