1.create ECMpy environment using conda:
$ conda create -n ECMpy python=3.6.5
2.install related packages using pip:
$ conda activate ECMpy
$ pip install cobra==0.13.3
$ pip install plotly
$ pip install -U kaleido
$ pip install nbformat
$ pip install requests
$ pip install Bio
$ pip install scipy
$ pip install ipykernel
Modeling Process
kcat from AutoPACMEN:iDL1450_get_data/reaction_kcat_MW.csv
kcat from DLKcat:get_reaction_kcat/kact/DLKcat3.30.cav
kcat from TurNuP:get_reaction_kcat/kact/TurNuP.csv
01_Constuct eciyw1475_AP.ipynb
Construction of eciYW1475_AP.
01_Constuct eciyw1475_DLKcat.ipynb
Construction of eciYW1457_DL.
01_Constuct eciyw1475_TurNup.ipynb
Construction of ecMTM.
02_CDF_kcat_and_mw.ipynb
Cumulative distribution of kcat and molecular weights. 03_FVA.ipynb
Comparative flux variability analysis.
04_PhPP_analysis.ipynb
Phenotype phase plane (PhPP) analysis.
05_trade-off.ipynb
Overflow metabolism simulation. 06_Substrte cascade utilization.ipynb
Substrte cascade utilization prediction. 07_metabolic_engineering_targets.ipynb
Metabolic engineering targets prediction.