When will sbmlimport support sbml level 3?

Would be useful to know. I believe 2020b only supports level 2, correct?

Has anyone else run into having to use an sblm level 3 model? How do you handle this?

Thanks.

Answer 1

[Arthur Goldsipe]

SimBiology already supports SBML level 3 version 1. That was introduced in R2016a. You can read more about what is supported here.

[Jim Bosley]

Arthur,

Thanks. I'm still a little confused. I was prompted to ask the question by the following exchange:

> mc = sbmlimport('SBMLModel.xml')

Error using SimBiology.internal.sbml.read

This version of SBML cannot be read. SimBiology supports the reading of SBML file versions up to Level 2 Version 1.

Error in privatesbmlio

Error in sbmlimport (line 89)

ret = privatesbmlio('read',nargout,{tempFileName})

It could be that my sbml is not conformal. Frank Bergmann and his friends have an online sbml tester that shows some errors. But in any case the error message is confusing.

Best,

Jim

PS: This is in R2020b running on Ubuntu.

[Arthur Goldsipe]

Ah, thanks for pointing that out. The error message did not get updated when support was added for SBML level 3. I will put this in our bug tracking system so that we can fix it in an upcoming release.

FWIW, SimBiology reports this error when libSBML returns the error code InvalidSBMLLevelVersion when parsing an SBML file.

[Jim Bosley]

I thought that must be the issue. So perhaps my sbml file is version 2. I'll go back to the source.

Any idea when version 2 will be implemented?

As always, thanks for the fast, understandable answers Arthur.

[Arthur Goldsipe]

Yes, if your file is level 3 version 2, that would explain the issue. I don't think a whole lot changed between version 1 and 2, so you might just try hand-modifying the version to 1 and see what happens (ideally running through the SBML validator to see if that flags anything else). I think another users have managed to do that with some success.

I'll pass along your request to upgrade our support to include level 3 version 2. We haven't hard much about customers needing this, so we've focused our work on things we consider higher priority. But now that we know it would be useful, we can consider this for a future release. Unfortunately, I can't comment here on any specific release data.