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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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CarveMe output interpretation #143

Closed iuliachiciudean closed 2 years ago

iuliachiciudean commented 2 years ago

Hi Daniel, Hi everyone,

I am a newbie in working with GEMs. I am trying to figure out how to make sense of the CarveMe output and I have a few (most likely, stupid) questions:

  1. Where to find the exact reactions and metabolites added by gap-filling option? I've carve the same .faa file without and with -g M9 and it tells me that some reactions and metabolites are added when using M9 for gap filling, but I don't know where to look for them.

  2. If I use the "gap-filling" option then the model will be constructed only by using the compounds in the media (ex. M9)? If so, then why do I obtain a greater FBA value for the gap filled model (M9) than for the gap unfilled model?

  3. Is there any way to visualize (in a friendly manner) the CarveMe outputs?

  4. Can you please recommend some publications or courses that explain how to deal with the GEMs info. I am planning to use CarveMe and SMETANA in order to figure out the microbial interactions in a bacteria community. But for now, I cant manage to understand the CarveMe outputs for a single organism :). Any help will be very welcome!!!!

Thank you very much. iulia

cdanielmachado commented 2 years ago

Hi Iulia,

Some answers to your questions below :)

  1. If you open the SBML file in a text editor these will be the last reactions in the file, and they will come with a text annotation that says GAP_FILL.
  2. Regardless of gap-filling, all models are generated without a defined medium. All uptake reactions are unconstrained by default. Your gap-filled model has a higher growth rate because it has more reactions and better yields. Use -i flag (followed by medium ID) if you want to initialize the model with the same medium you used for gapfilling.
  3. The output is a genome-scale metabolic network, so... not really.
  4. If you are new to the genome-scale metabolic modeling field, I always recommend starting with this paper: https://www.nature.com/articles/nbt.1614

Best regards, Daniel

iuliachiciudean commented 2 years ago

Hi Daniel,

Thank you for the answers and for the article recommendation.

I am not sure I understand the -i flag. What does it mean "to initialize the model with the same medium you used for gapfilling"?

Please let me know if this is correct:

Is this correct? Do I also have a model.xml -i M9 command?

Thank you. iulia