Sam Seaver
Sam Seaver
I had to make these changes to make the code work, but there's a chance that I got it wrong
It appears that a reaction that is empty, i.e. does not have products or reagents, is available in the microbial templates: ``` ModelSEEDDatabase/Templates$ grep rxn14003 */* | cut -f1,2,3,4 Core/Reactions.tsv:rxn14003...
Can we limit all checks in Travis to non-obsolete reactions/compounds?
It's been reported that there's are template mappings between a reaction's EC number and the EC number of the functional role its linked to in the template complexes. Here's an...
I've just discovered two pairs of reactions that use NADH and NADPH but deltaG is wrong for the second (NADPH) one: ``` seaver@twig:~/Projects/ModelSEEDDatabase/Biochemistry$ cat reactions.tsv | cut -f1,8,9,10,15,16 | grep...
This is a placeholder to remind us to discuss how we'd want to update and curate any reaction direction and thermodynamic reversibility in the biochemistry and in the templates. We...
Firstly, I'm not going to attempt to fix this reaction directly right now, though I've now come to understand what happened, as it's only available in the plant template. This...
This issue concerns reactions where the one or more reagents are proteins, typically with a side-group/chain that's involved in the reaction, and the status indicates a charge imbalance. A recent...
This is from an old email of Chris' that I left open, I'm initiating some of this via a commit coming today, but posting Chris' email as a placeholder of...
I put together the test code below based on a few things I read, and it seems like it would work, but I keep getting this error: ``` Traceback (most...