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I've noticed that when importing a omex archive in pymetadata, that it complains on windows about entries missing in the manifest, even though they are present.
Looking through the code, this is d…
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I noticed some strange behavior with someone else's code that uses `copy.deepcopy` to clone an OME object. I tried the pydantic-provided `model_copy(deep=True)` method and had the same bad results. Th…
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Hi,
I am using a genome-scale model and it's format is ".omex". Does anyone know how can I properly import the model in Matlab cobratoolbox?
I tried opening the file az a zip and importing the ".xml…
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Repeat exercise from issue #57 for a more (later) BioModels (ideally those that have SBML files that were generated by the authors).
Picked with help of [BioModels results table](https://github.co…
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# Provide required information needed to triage your issue
`Office.addin.setStartupBehavior(load)` fails on some files which seem to be corrupted.
- Issue replicates on specific files, and only …
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Allow to read all SBML files from a given OMEX file.
Necessary to register an additional file filter for `*.omex` and read the SBML files from the manifest file.
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The following links are not found:
http://co.mbine.org/standards/omex
http://co.mbine.org/standards/kisao
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Attached are a list of amici failures on the current suite of biomodels from https://github.com/sys-bio/temp-biomodels/tree/main/omex_files
Also included is the list of tellurium failures, because …
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After fixing issues with the [create_omex](https://github.com/robertvi/SBMLShowcase/blob/2c38d1abe0542196ed51e45f3e1f24b4c73e2e1e/utils/__init__.py#L44) function [#3](https://github.com/robertvi/SBMLS…
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[Attached](https://github.com/sbmlteam/libCombine/files/6682839/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint.zip) is an OMEX archive with a malformed OMEX meta file (`metadata.rdf`).
How can…