Unable to read in copasi files

[ethanmizuno16]

When trying to import an SBMLDiagrams image as an xml into copasi, after it is exported back into SBML, the program is unable to recognize the layout and render settings that are changed after the image has gone through copasi, therefore making it impossible to reproduce images from copasi.

[SunnyXu]

Ethan, the SBML file you sent to me has warning errors. COPASI could tolerant to it, however, SBMLDiagrams cannot load it with a given warning message.

[SunnyXu]

[SunnyXu]

Note the file is L2V4. Currently, cannot fix this issue due to libSBML.

[hsauro]

Can you ask Lucian about this? You can't just leave it.

H

On Fri, Oct 6, 2023 at 10:23 AM Jin XU @.***> wrote:

Currently, cannot fix this issue due to libSBML.

— Reply to this email directly, view it on GitHub https://urldefense.com/v3/__https://github.com/SunnyXu/SBMLDiagrams/issues/87*issuecomment-1751148717__;Iw!!K-Hz7m0Vt54!j-GlQu0ApgXTBtVnWHCQHaTmuoGpPvqh1b3FwONtVxcFiPZ7Ri_ySRKMgTsTxQN5GMXXsxV4_7AET1Ij7GRWFfu0vttB6g$, or unsubscribe https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AAIBSDWEXWKSA3DHOHVNEX3X6A5AHAVCNFSM6AAAAAA5N5HDL6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONJRGE2DQNZRG4__;!!K-Hz7m0Vt54!j-GlQu0ApgXTBtVnWHCQHaTmuoGpPvqh1b3FwONtVxcFiPZ7Ri_ySRKMgTsTxQN5GMXXsxV4_7AET1Ij7GRWFfuCkjGJ2A$ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

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[SunnyXu]

I am not sure why Ethan is generating an SBML file in L2V4, this is not the main point of SBMLDiagrams dealing with level 3 with layout and render.

[hsauro]

Can you talk to him about it?

On Fri, Oct 6, 2023 at 3:32 PM Jin XU @.***> wrote:

I am not sure why Ethan is generating an SBML file in L2V4, this is not the main point of SBMLDiagrams dealing with level 3 with layout and render.

— Reply to this email directly, view it on GitHub https://urldefense.com/v3/__https://github.com/SunnyXu/SBMLDiagrams/issues/87*issuecomment-1751468728__;Iw!!K-Hz7m0Vt54!nwVi4JgZdX3otqOV0eI6R0JhLyi9780wtDQmwTt8MJpPb526wKxkTkTPen-h4-s4Bzf0w5S4317jHfyTIbTFYpI26NXMww$, or unsubscribe https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AAIBSDXUY4CP74CDW2FX4KTX6CBINAVCNFSM6AAAAAA5N5HDL6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONJRGQ3DQNZSHA__;!!K-Hz7m0Vt54!nwVi4JgZdX3otqOV0eI6R0JhLyi9780wtDQmwTt8MJpPb526wKxkTkTPen-h4-s4Bzf0w5S4317jHfyTIbTFYpJ0Q082ow$ . You are receiving this because you commented.Message ID: @.***>

[SunnyXu]

Hi Ethan, pls try to export SBML files from COPASI by choosing "Save as Type" as "Level 3 Version 1" instead of "Level 2 Version 4". Please note that SBMLDiagrams is dealing with SBML level 3 with layout and render.

[hsauro]

That’s a good point. Jin you should say, if you don’t already, on the readme on GitHub, that we only support level three.

H

On Wed, Oct 11, 2023 at 5:07 PM Jin XU @.***> wrote:

Hi Ethan, pls try to export SBML files from COPASI by choosing "Save as Type" as "Level 3 Version 1" instead of "Level 2 Version 4". Please note that SBMLDiagrams is dealing with SBML level 3 with layout and render.

— Reply to this email directly, view it on GitHub https://urldefense.com/v3/__https://github.com/SunnyXu/SBMLDiagrams/issues/87*issuecomment-1758718603__;Iw!!K-Hz7m0Vt54!iznQNoavEla4SSMPehQikSHmrkyFt_g_rQCW8DOc_bdW7ojz9gTt99N-PvkleV-Cpg7PjxRtdD3jkCda3IRaaDJJ0jkVWQ$, or unsubscribe https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AAIBSDTESUX3OGPWM6SGECDX64YFVANCNFSM6AAAAAA5N5HDL4__;!!K-Hz7m0Vt54!iznQNoavEla4SSMPehQikSHmrkyFt_g_rQCW8DOc_bdW7ojz9gTt99N-PvkleV-Cpg7PjxRtdD3jkCda3IRaaDKaN9TlYw$ . You are receiving this because you commented.Message ID: @.***>

-- Herbert Sauro, Professor Director: NIH Center for model reproducibility University of Washington, Bioengineering 206-685-2119, www.sys-bio.org, http://reproduciblebiomodels.org/ Mobile: 206-880-8093 @.*** Books: http://books.analogmachine.org/