Thomas Zajac

This most likely stems from ModelPolisher currently not being used to polish the models, due to issues with the latest release, as both the listOfFluxObjectives and refseq_ issue should be...

Currently fixing small issues still existing with ModelPolisher and running polished Models through the Validator to check for further issues. If everything goes well, we could have a ModelPolisher release...

Seems to be an issue with ModelPolisher, might have to do with the way how the annotation URIs are constructed. URL_Prefix is correct, but we somehow use the bigg_id inchi_key...

Sure, I'll change that.

Which options did you use when running ModelPolisher? I get 52 groups in one ListOfGroups for this model, so that is strange

I had a look at the code and BiGG. Subsystem information is currently retrieved based on model and reaction BiGGId, as the information is stored in the model_reaction table. I...

- **assigned_to**: nobody --> niko-rodrigue - **labels**: --> XML Reading/Writing - **status**: open --> pending-works-for-me Original comment by: niko-rodrigue

Did you get a NullPointerException ?? The original XMLNode of the message is set in the SBMLCoreParser when an element message is encountered, the same way as the typeOfNotes is...

- **status**: pending-works-for-me --> open-works-for-me Original comment by: sebfroh

Okay, I think I get it. The namespace used for messages is "http://www.w3.org/1999/xhtml". The parser for this namespace is StringParser (file PackageParserNamespaces.xml): line: <entry key="http://www.w3.org/1999/xhtml"> org.sbml.jsbml.xml.parsers.StringParser </entry> The Code in...