ModelSEEDDatabase

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Wrong name for cpd00874

1

Hi the stereochemistry of cpd00874 shows it should be named `(3R,5R)` / `D-erythro`. Currently, it has all possible stereo names, i.e. `(3R,5R)` / `D-erythro` and `(3S,5S)` / `L-erythro` What is...

smoretti

freiburgermsu

Hi, I could not figure out how I will dump/extract ComplexRoles.tsv and TemplateReactions.tsv files which are needed for using in PyFBA module. I have tried to run the DumpSOLRTables_Master.pl via...

tfb-sv

Use of extra boundary reactions, metabolites, and introduction of _b suffix

1

I noticed recently that the models generated via all of the modelseed services have explicitly-represented boundary metabolites rather than the standard use of a true boundary (e.g., standard is extracellular...

gregmedlock

Hi we found several issues with aerobactin compounds in ModelSEED. - cpd26452 SMILES looks to be invalid according to chemaxon and smiles drawer at least. Should be something like `CC(=O)N(O)CCCC[C@H](NC(=O)CC(O)(CC(=O)N[C@@H](CCCCN(O)C(C)=O)C([O-])=O)C([O-])=O)C([O-])=O.[Fe]`...

smoretti

Nwchem mol2

4

I added the NWChem optimized structures (mol2) of Yeast with partial charges computed with Mulliken population.

nkkchem

Hi it looks **cpd27117** and **cpd28855** are fake entries; certainly used in MetaCyc at import time by ModelSEED for testing purposes.

smoretti

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...

samseaver

checking duplicates in Travis

3

Can we limit all checks in Travis to non-obsolete reactions/compounds?

samseaver

Hi I wonder if (S)-3-Hydroxyisobutyrate (cpd19043) and (S)-3-Hydroxyisobutyric acid (cpd23281) are really what they are supposed to be. - (S)-3-Hydroxyisobutyrate (cpd19043) and (S)-3-Hydroxyisobutyric acid (cpd23281) have different stereochemistry. They look...

smoretti