GSM to ASM - mauriceling/advancesyntoolkit GitHub Wiki

Synopsis: Converts a genome-scale model (GSM) to ASM-bassed kinetic model using Amir-Hamzah, N, Kuan, ZJ, Ling, MHT. 2022. Kinetic Models with Default Enzyme Kinetics from Genome-scale Models. Acta Scientific Computer Sciences 4(1): 59-63.

Usage: python astools.py GSM-to-ASM [options]

where options can be

• model: Model acceptable by Cameo (see http://cameo.bio/02-import-models.html).
• name: Name of model author / creator.
• outputfile: Relative path to the write out the converted ASM model.
• metabolite_initial: Initial metabolite concentration. Default = 1e-5 (10 uM).
• enzyme_conc: Enzyme concentration. Default = 1e-6 (1 uM)
• enzyme_kcat: Enzyme kcat / turnover number. Default = 13.7 (13.7 per second) based on Bar-Even et al (2011, 2015).
• enzyme_km: Enzyme Km (Michaelis-Menten constant). Default = 130e-6 (130 uM) based on Bar-Even et al (2011, 2015).

For example,

python astools.py GSM-to-ASM --metabolite_initial=1e-5 --enzyme_conc=1e-6 --enzyme_kcat=13.7 --enzyme_km=130e-6 --model=e_coli_core --name=e_coli_core --outputfile=models/asm/e_coli_core.modelspec