importing ".omex" models

[Laminsecin]

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" file inside but there is an error with the met charges and the genes matrix is also missing.

I hereby confirm that I have:

• Tried to solve the issue on my own
• Retried to run my code with the latest version of The COBRA Toolbox
• Checked that a similar issue has not already been opened

[rmtfleming]

Do you mean omix? https://www.omix-visualization.com

…

On Wed, 28 Dec 2022 at 12:07, Laminsecin ***@***.***> wrote: *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" file inside but there is an error with the met charges and the genes metix is also missing. * *I hereby confirm that I have:* - [X ] Tried to solve the issue on my own - Retried to run my code with the latest version of The COBRA Toolbox - [X ] Checked that a similar issue has not already been opened *(Note: You may replace [ ] with [X] to check the box)* — Reply to this email directly, view it on GitHub <#2104>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAQMEOX2CGL4XLYSEUCVOFLWPQURJANCNFSM6AAAAAATLGSGTU> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- -- Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D. ---------------------------------------------------------------------------- Associate Professor, School of Medicine, National University of Ireland, Galway. & Assistant Professor, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University. https://www.universiteitleiden.nl/en/staffmembers/ronan-fleming ---------------------------------------------------------------------------- Peer-reviewed publications: https://goo.gl/FZPG23 Mobile: +353 852 109 806 Skype: ronan.fleming ---------------------------------------------------------------------------- (This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)

[Laminsecin]

Do you mean omix? https://www.omix-visualization.com

No sir it's a COMBINE archive format and here is the link to it: https://www.ebi.ac.uk/biomodels/MODEL2102050001#Files

[tpfau]

As mentioned on the OMEX description, omex files should essentially be a zip format.
I would try open it with an some form of zip-tool (potentially changing the ending to .zip). THen there should be an sbml file in there, as described in the Article introducing omex:
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-014-0369-z
This sbml should be importable via the readCbModel function

[Laminsecin]

Thank you so much for your explanation.

[draeger]

I successfully tried the following steps:

1. Download the file again from BioModels
2. Rename the file from iCGB21FR.omex to iCGB21FR.zip
3. Unzip it and navigated inside the newly created folder, where the file iCGB21FR.xml (the SBML model) is located.
4. Check that model file with the SBML validator.

The validator stated that it is entirely valid (just some warnings are issued, which can be safely ignored). The validator also recognizes it as a flux-balance constraints model. Consequently, it should run in a COBRA-compliant software. We tested it using COBRApy where it worked.

[Laminsecin]

Dear Dr. Draeger,
Thanks for your kind respond. I actually just found out that I only face these errors in MATLAB COBRA toolbox version 2.
As I installed version 3, the model was correctly loaded.

[draeger]

Excellent! I am glad this works now. In the longer term, adding direct support for the OMEX file format could be a valuable feature for COBRA Toolbox because it can ship Models, Figures, Data, Escher Maps, and much more, all bundled together.