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Hi,
Thanks for this pipeline. I am at the same time looking at m2m. I wonder how to generate a "seed" file in .xml especially if I have no idea about the medium that would be used for the communit…
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Hi,
I am having trouble with navigating with modelSEED model since it has IDs different from IDs of BiGG-based models (sample reaction ID in my model is rxn00974_c0). Unfortunately, the modelSEED m…
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Hi, jotech, thanks for providing that media file, seems that composition of my media was wrong, now the growth rate is 0.056.
However now the xml file generated is showing valid by sbml validator b…
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### Description of the issue:
While I was checking the reactions with a confidence score lower than `3`, I've found that some of the reactions with KEGG ID's are not the same as shown in KEGG Reactio…
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We need to add the forked versions of cobrapy and optlang that contain the COINOR-CBC and OSQP solvers.
This was the way that I installed them for testing. We can probably run the installs for optl…
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Both reactions in pyridoxal-phosphate metabolism are defined as reversible, but thermodynamics should allow only one direction. Reaction `name`, `id`, and `reaction` definition should be updated accor…
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This issue will serve to be a place-holder for the list of things I need to check in the Biochemistry database, to ensure its quality.
Generally speaking, there's several goals for the biochemistry:
…
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Hi,
As some of you are aware, I'm working with @eladnoor to apply the component contribution method to the entire MetaNetX database and thus extend the content in equilibrator. We are successfully …
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Apologies if this is actually a trivial error on my part - it's my first time playing around with COBRA / metabolic models.
I am using ModelSEED to generate a SBML model of _Vibrio natriegens_ and …
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Hi all,
Thanks for your great job. I have a question concerning the direction of a reaction.
The reaction rxn00068 should be to this direction `