johan-gson
johan-gson
### Description of the issue: MAR08430: creatine-phosphate[m] => creatine-phosphate[c] According to wikipedia (https://en.wikipedia.org/wiki/Creatine_phosphate_shuttle, not a great source, but probably ok) this transport goes via diffusion, which means it is spontaneous....
### Description of the issue: The current code is problematic since it uses "which('reactions.tsv')" - if we use for example the mouse model, it will grab the file for Human-GEM...
### Description of the issue: There are two metabolites in the model called galactose-1-phosphate[c] alpha-D-galactose-1-phosphate[c] According to https://pubchem.ncbi.nlm.nih.gov/compound/alpha-D-Galactose-1-phosphate, these are synonyms These are then duplicates (interestingly, they have slightly different...
### Description of the issue: - [ ] These two reactions are probably the same, but different stoichiometry. They have the same GPR. MAR01364, MAR03880: arachidonate[c] + O2-[c] => 12-peroxy-(5Z,8Z,10E,14Z)-eicosatetraenoate[c]...
### Description of the issue: The metabolite (S)-dihydroorotate[c] is reported to be exported by cells (see https://www.nature.com/articles/s41467-018-08033-9 ), but there is no export rxn (and I assume there should be...
### Description of the issue: Some reaction pairs are very similar, but with different stoichiometry, which is suspicious: We should figure out which is right. The third column is if...
This PR fixes issue #401 and now allows for specifying the paths to the tasks and reactions.tsv. This is good when using the code for for example Mouse-GEM. ### Main...
### Description of the issue: We should add export of succinate from cells and mitochondria. There is some evidence for that, for example: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7273505/ Also, that complex II can be...
### Description of the issue: I'm currently working with GECKO3, and one of the ideas there is to work with the EC field in the model directly instead of identifying...
Also adapted the code to be able to handle Human-GEM in addition to Yeast-GEM. I have not tested the code with Yeast-GEM. The code is not well tested at this...