chaowu88/zymomonas_modeling

zymomonas_modeling

substrate_uptake_kinetics.py estimates the kinetic parameters of glucose facilitator protein (glf) which transports both glucose and xylose with competitive inhibition of each other.
Required input file: measured_kinetics.xlsx

constrained_MDF_and_EPC.py performs thermodynamics analysis which maximize the minimal driving force and enzyme protein cost analysis which minimize the totol enzyme protein cost of a given pathway with additional metabolite concentration constraints. This is as upgraded version of the functions in PathPaser.
Required input file: glucose_utilization_pathway.tsv or xylose_utilization_pathway.tsv

timecourse_MDF_EPC.py performs timecourse thermodynamics analysis and enzyme protein cost analysis with additional metabolite concentration constraints This is as upgraded version of the functions in PathPaser.
Required input files: glucose_utilization_pathway.tsv or xylose_utilization_pathway.tsv, kinetic_data.tsv (generated by substrate_uptake_kinetics.py)

dfba.py simulates growth of Zymomonas mobilis using dynamic flux balance analysis, and compares performance under various substrate ratios and agitation rates.
Required input files: zymo_BDO_deltaPDC.json, measured_kinetics.xlsx