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It looks like the cache in the PATRICStore object is allowed to grow to unlimited size. This isn't a problem when running as an app since everything goes away when the app ends. But when running in …
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I reported this in kbase too. No data is returned for /chenry/public/modelsupport/media/Complete. It's particulaly confusing since complete media is the default.
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@samseaver, I'm confused on the compounds.master.tsv and reactions.master.tsv files in the Biochemistry directory. I ran the Print_Master_Reactions.pl script and it generated a Master_Reaction_List.t…
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Should all compounds in reactions have compartments?
I see "Pseudomonas aeruginosa LPS core precursor 2" in rxn13866 doesn't:
https://www.patricbrc.org/api/model_reaction/?http_accept=application/j…
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I'm trying to make compounds in equations linkable as in the following screenshot, but there's no easy to way to do this since the order of ids is different from the order of names.
Here's an example…
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Just a reminder that the Print_Master_Reactions_List.pl script requires a Bio::KBase::ObjectAPI::KBaseBiochem::Reaction object that has a genEquationCode() method.
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There are 1088 compounds in the Biochemistry/compounds.default.tsv and Biochemistry/compounds.master.tsv files where the value of the the deltag field is "deltaG" and the value of the deltagerr field …
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A "Bad reference" error is now returned for every attempt to access a ModelSEED object in my store. I traced the bug to the ModelSEED::Reference::_build_schema() function, seems like a `$schema->{typ…
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The model runfba command gives this error:
$ model runfba my-model --html
Global symbol "$mapping" requires explicit package name at /home/mmundy/ModelSEED/ModelSEED/lib/ModelSEED/MS/Factories/Exchan…
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So I do this (simplified):
```
foreach my $pwy (sort keys %$Pathways){
$biochem->add("reactionSets",{id=>$id
type=>'KEGG',
clas…