KO and OE genes in human model

[sarit feldman]

Hi everyone!

I have a list of genes and would like to find the best combination of knockout or overexpression in the list for my objective.

I started with RECON1 and a list of 10 genes. I validated  that the genes exists in the model.

I'm now trying to KO genes for start, but I'm unable to do even deletion of one gene.

I've tried for example model.genes[0].knock_out() and deletion._multi_deletion(model, "gene", [['HADHA'], ['CPT1B']],method= "fba"). The first returns None as the new model, the second isn't working. 

I'm running the 

Can anyone help please?

Thank you!

[sarit feldman]

I was successfull with using _multi_deletion.

The problem is it only returns the df with growth rate and solution status.

how can i get the solution itself?

i would like to change the objective and measure it.

ב-יום שני, 6 במאי 2024 בשעה 16:01:55 UTC+3, sarit feldman כתב/ה: