Eduard Kerkhoven

1. Looking at the specification of Cobra model that you linked, they also indeed be in `rxnReferences`, for both Cobra and Raven. Also, there it specifies that `rxnReferences` is "Column...

Irrespective, pubmed IDs don't need to be prefixed with `pmid:`. This is done for ChEBI as it really is part of the identifier ([here, CHEBI:17234](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17234)), not because it would otherwise...

Perhaps then also start an issue at Cobra, because they do [state](https://github.com/opencobra/cobratoolbox/blob/master/docs/source/notes/COBRAModelFields.md) that `rxnReferences` and `rxnNotes` are separate fields?

As far as I know the yaml format from RAVEN and cobrapy are not identical. - [ ] RAVEN does not yet output metadata (#311), while cobrapy does includes in...

@tpfau Just to confirm, you are using MATLAB 2017b?

I now also run Matlab 2017b on Windows and I cannot reproduce the error, neither before or after #76. @danieljcook can you please check whether you still get this error...

@simas232 Exactly, works well with both your provided toyModel as well as real models. Just realize that I don't have any additional Matlab Toolboxes installed, perhaps this means that I...

The problem is in `MATLAB\R2017b\java\jarext\tika-app.jar` containing conflicting Java libraries. The Apache POI libraries provided by RAVEN are version 3.8, while the MATLAB provided are of version 3.17. Between these versions,...

While removing Text Analysis Toolbox is a workaround, this is not a solution for users without sufficients rights on their computer (e.g. students on university computers). So it would be...

The graph has been shown in previous publications (e.g. yeast8 [Supplementary Figure 4C](https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-019-11581-3/MediaObjects/41467_2019_11581_MOESM1_ESM.pdf)), and is generated by [this function](https://github.com/SysBioChalmers/yeast-GEM/blob/main/code/modelTests/growth.m). It uses [this data](https://github.com/SysBioChalmers/yeast-GEM/blob/main/data/physiology/chemostatData_Tobias2013.tsv), which was gathered in [Österlund _et al._...