How to save model with added reaction in jupyter

[Karen Chung]

Hi there,

I notice that, after I add reactions to the model in the Jupyter notebook. The next time, when I open the same .ipynb file, I'll need to re-import model then the reactions that added previously all gone? Like it did not saved the changes I made to the model. 

Kindly advise. 

Regards,
Karen

[Moritz Beber]

Dear Karen,

You need to save your changes to SBML again (I assume) by calling the write_sbml_model function (https://cobrapy.readthedocs.io/en/latest/autoapi/cobra/io/index.html#cobra.io.write_sbml_model).

Best,

Moritz

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[Karen Chung]

Hi Moritz,

May I ask how to do I write for the filename?

cobra.io.write_sbml_model(cobra_model, filename, f_replace=F_REPLACE, **kwargs)[source]

[Piyush Nanda]

  Hi,

You need to use:

cobra.io.write_sbml_model(model,'ATCC700603model.xml')

Regards,

Piyush

[Karen Chung]

Hi Piyush, yes it works. Thanks for your reply!

Thank you both for your help!

Regards,
Karen