SiYeon-Ju/iBridge

iBridge

#iBridge #Project This project is to identify target reactions or metabolites that will enhance production of commercial chemicals through a metabolite-centric approach

##Example

1. Clone the repository

    git clone https://github.com/kaistsystemsbiology/iBridge.git
   

2. Change the directory

    cd ibridge
   

3. Create and activate virtual environment

    conda env create -f environment.yml
    conda activate ibridge
   

4. Install the virtual environment kerenl into the jupyter

    python -m ipykernel install —user —name ibridge —display-name "ibridge"
   

FSEOF, FVSEOF, OptForce simulation

1. Create and activate virtual environment

    conda env create -f environment2.yml
    conda activate metool
   

2. Run FVSEOF

    python ME_targeting.py -i ./input/ijo1366_IRR_indirubin.xml -o ./output/fvseof -t EX_INDIRUBIN_LPAREN_e_RPAREN_ -b Ec_biomass_iJO1366_core_53p95M -m fvseof
   

3. Run FSEOF

    python ME_targeting.py -i ./input/ijo1366_IRR_indirubin.xml -o ./output/fvseof -t EX_INDIRUBIN_LPAREN_e_RPAREN_ -b Ec_biomass_iJO1366_core_53p95M -m fseof
   

4. Run OptForce

    python OptForce.py