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m-jahn / genome-scale-models

Genome scale metabolic models in SBML format
GNU General Public License v3.0
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Software to be? #14

Closed arianccbasile closed 1 year ago

arianccbasile commented 1 year ago

Hello :) I really like your resource but I tried to apply it to other models, with minor edits, but it stopped. It seems is a very model-specific resource. Are you planning to make it as a more universal tool?

Best, Arianna

m-jahn commented 1 year ago

Hi Arianna,

Thanks for your interest in the model. Can you be more specific with the issues you encountered? This repo contains a genome scale model for Ralstonia eutropha aka Cupriavidus necator. It's a static file in the end - what exactly do you mean by "tried to apply it to other models"? In which way did it stop? Yes this is a model specific resource, it's actually just a the model that you need, ideally.

Maybe you misunderstood that you have to run the python code yourself. This is not necessary, only to recreate the steps to parse and modify the original model from Park et al. If you want to work with the model, just download it here: https://github.com/m-jahn/genome-scale-models/tree/master/Ralstonia_eutropha/sbml

Then follow the steps explained in the Readme.

arianccbasile commented 1 year ago

I was trying to use this tool on a model I am creating. However, I get this error. Yeah, I understand. I was just trying to adapt to my needs but it is actually not doable. Thank you for answering tho :)

`Traceback (most recent call last): File "/Users/arianna/miniconda3/envs/carveme2/lib/python3.8/site-packages/cobra/core/dictlist.py", line 452, in getattr return DictList.get_by_id(self, attr) File "/Users/arianna/miniconda3/envs/carveme2/lib/python3.8/site-packages/cobra/core/dictlist.py", line 57, in get_by_id return list.getitem(self, self._dict[id]) KeyError: 'TYRTA1'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "upgrade_main.py", line 66, in main() File "upgrade_main.py", line 36, in main um.modify_reactions(model) File "/Users/arianna/Documents/programs/genome-scale-models-master/Ralstonia_eutropha/upgrade_model.py", line 140, in modify_reactions model.reactions.TYRTA1.id = 'TYRTA' File "/Users/arianna/miniconda3/envs/carveme2/lib/python3.8/site-packages/cobra/core/dictlist.py", line 454, in getattr raise AttributeError("DictList has no attribute or entry %s" % attr) AttributeError: DictList has no attribute or entry TYRTA1 `

m-jahn commented 1 year ago

No this is not doable. You might had in mind to update your model with similar code, but this is really highly specific for Ralstonia. Your model probably does not have a reaction called TYRTA1 (and many others), so there's no point to use the code for other models.