Blocked Biomass Reaction in xls2model

[Kenan Jijakli]

Hi

I have an Excel formatted model. Whenever I specify a biomass reaction by inputting '1' in the 'Objective' column, that reaction gets blocked. Whenever I unspecify it by changing '1' to '0' it gets unblocked. I tried specifying different reactions as the objective function and this persistently happens. For instance, if I specify the ATP maintenance reaction as the objective function, it becomes blocked, and if I unspecify it gets unblocked again.

Yesterday my computer crashed and I had to reinstall Matlab (R2016b) and Cobra. Just before that, I was using Cobra with the same exact model and it was working fine. It might be worth mentioning that as soon as I execute xls2model, I get a message that says "Excel is not installed; limit of 10000 reactions." then the model loads. I wasn't getting this message before my computer crashed.

If anyone can help in anyway I would be deeply grateful.

Thanks,
Kenan

[Laurent Heirendt]

Hi Kenan,

How many reactions does your model have? There is a limit of reading xls files for very large models in order to avoid out-of-memory issues.

May you attach the output of >> generateSystemConfigReport?

Thanks,

Laurent

[Kenan Jijakli]

Thank you Laurent for your response.

My model has 617 reactions. I figured out something actually. If I designate the objective function with a '-1' instead of a '1', it doesn't get blocked, the model runs, and solves a maximization problem. However, I am not really sure why that works.

I also attached the log file.

Let me know if you have any ideas or advice.

Thanks,
Kenan

[Laurent Heirendt]

Hi Kenan,

Great to hear that you managed to read in the model.

Best,

Laurent

[Thomas Pfau]

Hi Kenan,

Thanks for reporting this. This is actually a bug in the xls IO, where the objective was being flipped (thus a normal optimization would yield 0 flux == minimal value) . I'm currently correcting this and putting in a pr that should fix it.

Best

Thomas

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[Kenan Jijakli]

Thank you Thomas for letting me know. And thank you and all the other developers for your efforts.

Regards,
Kenan