Ask Pathway Tools logo   Pathway Tools Question & Answer forum for SRI's Pathway Tools

Ask Your Question

SBML Import

asked 2019-12-18 18:10:12 -0500

dnnunn gravatar image

May be dense but cannot find the option in the File>Import to do an SBML import as is reported to be a capability for quite some time.

Can't yet upload an image file (not enough Karma) but am seeing: Frames from Spreadsheet Format File Frames from Lisp-Format File DB Links from File Citation from PubMed Protein Features from UniProt (greyed out) Phenoytype Microarray Data from Spreadsheet or OPM Taxa in the NCBI Taxonomy DB Entire DB from a tar file Test PGDF from File in Drop Box PGDBs from the Registry

but nothing to import SBML file

Thanks for you help/advice

edit retag flag offensive close merge delete

1 Answer

Sort by ยป oldest newest most voted

answered 2019-12-20 10:53:49 -0500

Suzanne Paley gravatar image

Are you using Windows? This capability seems to be disabled for Windows (I can see the command there, on my Mac). I personally don't know the reason for that -- presumably it's some issue with one of the libraries we use, which is perhaps not available for Windows.

edit flag offensive delete link more


Thanks Suzanne, yes I am using Windows. Any chance this would be something that can be addressed with a fix? Or should I try to find a Mac to do the conversion, export into a compatible format and import?

dnnunn gravatar imagednnunn ( 2019-12-20 11:33:32 -0500 )edit

I'm not sure. I've forwarded your question to some other developers, but you may need to wait until after the holidays. If you have access to a Mac, you should be able to do the import, save the pgdb, and move it to someplace where your Windows machine can access it, but I don't know if that's the best/only approach.

Suzanne Paley gravatar imageSuzanne Paley ( 2019-12-20 20:20:40 -0500 )edit

I've been told that the 23.5 release (which is in the process of being released as we speak) will have sbml import enabled for Windows too.

Suzanne Paley gravatar imageSuzanne Paley ( 2019-12-21 22:37:48 -0500 )edit

Great news, thanks!

dnnunn gravatar imagednnunn ( 2019-12-22 15:09:32 -0500 )edit

Your Answer

Please start posting anonymously - your entry will be published after you log in or create a new account.

Add Answer

Question Tools

1 follower


Asked: 2019-12-18 18:10:12 -0500

Seen: 251 times

Last updated: Dec 20 '19