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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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Models created with CarveME fail in molecular weight of biomass products standardization #84

Closed arianccbasile closed 4 years ago

arianccbasile commented 4 years ago

Dear Daniel, I have created many models with your amazing source and now I want to check their consistency. Following the paper "Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models (https://academic.oup.com/bioinformatics/article/33/22/3603/3965323), I wanted to make sure that the molecular weight of the biomass product in each model is standardized. However, I tried both the Python script (not working at all due to the lack of a package called "metFormulae" that should be imported in line 8) and the Matlab script. The Matlab script works properly with the model provided in the paper but not with those created with CarveMe. Do you know why? Do you know of any other source to get this normalization?

Sincerely, Arianna Basile

cdanielmachado commented 4 years ago

Hi Arianna,

The universal model in CarveMe produces a biomass equation that is normalized to 1 gDW by default.

If you changed the biomass equation, you can use this python function to calculate the total molecular weight:

https://github.com/cdanielmachado/carveme/blob/7eb898a7abb3870c4206f496c62c9044901ba9e5/carveme/reconstruction/utils.py#L101

I hope this helps.

Best regards, Daniel

arianccbasile commented 4 years ago

It sounds super good. Thank you very much, Daniel.