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Several BiGG SBML models are invalid and cannot be easily read #366

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smoretti opened this issue Jan 23, 2020 · 4 comments
Open

Several BiGG SBML models are invalid and cannot be easily read #366

smoretti opened this issue Jan 23, 2020 · 4 comments

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@smoretti
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Hi

Several BiGG models are invalid in SBML format:

Thanks

@mephenor
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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 handled by it.
I am currently working on some remaining issues with regard to annotation and performance and adding thorough testing to at least the core parts so that it becomes usable once again.

@smoretti
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Thanks
Waiting for your fixes

@smoretti
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smoretti commented Mar 6, 2020

Any news for this fix?

@mephenor
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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 tomorrow and then the BiGG Models team can decide, if they want to use it once again in its current state.

The refseq_* annotations listed cannot be resolved, so they will be removed, if you run the model through ModelPolisher.

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