Closed wintermute221 closed 4 years ago
Hi @wintermute221,
COBRApy and cameo are two Python packages that can be used to study genome-scale metabolic models.
They are similar :
... but also different:
Anyway, you should have a look at their respective publications:
If you simply want to perform some FBA, I would recommend you to go with COBRApy. If you want more complex tasks and you know that those are already implemented in cameo, I would recommend you to try cameo.
You do not need to use COBRApy syntax to load models that you will use with cameo; I would recommend to load your model directly from an SBML file with the package that you intend to use (cameo or COBRApy).
cameo has also some great learning resources : https://biosustain.github.io/cell-factory-design-course/ and https://try.cameo.bio
Does that answer your question?
Awesome! Indeed answer all my questions. Thank you for that @bdelepine. Your explanation is very detailed and clear that I couldn't expect more. Really appreciate your time and thanks to that now I've got a better understanding of those two packages!
Yuhan
Hi! I've got a very basic question hoping someone could help me sort it out. I looked through the documentation of cameo and found several main differences between cameo and cobrapy, which could be concluded as i) Solver interface, ii) Importing a model, and iii) Solving models. However, I can't say I fully understand them pratically and I wonder whether it is right if I firstly use cobrapy command to load my model and then implement FBA by cameo command.
By the way, I also noticed that in the documentation there is a label saying 'build failing' and I wonder if it means cameo is not able to use.