WBM reconstructions, Harvey and Harvetta

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Subasree S

Mar 26, 2022, 2:58:54 PM3/26/22
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Hi all,
I am working on CBM of Recon3D. I used Harvetta model (Ines Thiele et al., 2020) today to simulate it on cobrapy for the very first time. I tried converting the .mat file but I could not do so due to the error which says that the LB should not be greater than UB for a reaction. It is not the case, LB is less than UB, 62168.8 < 93253.2. I have attached the screenshot.

Any suggestion to resolve this will be helpful.

Screenshot 2022-03-27 at 12.26.49 AM.png

Moritz Beber

Mar 27, 2022, 5:59:19 AM3/27/22
to cobr...@googlegroups.com
Hello Subasree,

It looks like cobrapy is using the default upper bound of 1000 for the comparison. That's a mistake. Can you please open on issue on GitHub? https://github.com/opencobra/cobrapy/issues

Thank you in advance.

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Subasree S

Mar 27, 2022, 10:51:23 AM3/27/22
to Moritz Beber, cobr...@googlegroups.com
Yes, it is very much possible.  Thank you. I will open an issue on this.

Thank you

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