Yu Chen

@BenjaSanchez I just used Yeast 7.6 to get flux distributions for Jianye's project and found increased fluxes through PPP pathway as growth rate increases. So Yeast 7.6 enables good flux...

@BenjaSanchez Yes, from sourceforge. I used the original version of Yeast 7.6 without any modifications.

@BenjaSanchez I just used experimental exchange fluxes (e.g. glucose, O2, CO2 for low growth rates, and glucose, O2, CO2, ethanol, acetate for high growth rates) as constraints and maximised growth....

I am not interested in any specific genes but just found in the T2T-CHM13 paper that 99 newly introduced genes were predicted to be protein coding, which (if involved in...

> Did you use the same DLKcat output file to make both a light and full ecModel? Yes

I just notice that the DLKcat output files generated by full and light protocols are not interchangeable due to rxn IDs in these two types of ecModels. I do not...

Could you assign me to the task here? With this function, we can not only manually curate kcat, e.g., using kmax, but also load kcat from GotEnzymes. The latter could...

Thanks for assigning me here! I just thought that the input of this function `readKcatTable` would be either 1) manually curated kcat values (the input file should contain model rxn...

In GECKO 1/2, I remember that the maximum kcat among all multiple EC codes of a reaction is selected for the reaction. Is it possible to just follow this in...

> This looks very good, and I agree with you on this modification: multiplying coefficient of enzyme in metabolic reaction by 1e3 (or 1e6) and coefficient of prot_pool in prot_pool...