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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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Does gap filling exclude new metabolite uptake reactions? #157

Open behzadk opened 2 years ago

behzadk commented 2 years ago

Hi Daniel,

I was looking into how the gap filling works. I saw that new exchange reactions have lower bounds set to 0. If I understand correctly, this means the gap filling ignores the possibility of uptaking new metabolites. Is there a reason for this?

https://github.com/cdanielmachado/carveme/blob/0f2f48de40fbb6ba6fc98ede73ae031af3263013/carveme/reconstruction/gapfilling.py#L34-L41

Thanks, Behzad