#425 Missing Qualitative Model information

[Sven Thiele]

Hello,
I'm using libSBML via the precompiled MATLAB Interface provided here:
https://sourceforge.net/projects/sbml/files/libsbml/5.13.0/stable/MATLAB%20interface/
I want to access the data of qualitative models as detailed in the SBML QualitativeModels package.
Unfortunately the MATLAB struct created by TranslateSBML() does not contain any of the data in our SBML files.

regards, Sven

[Michael Hucka]

Hi Sven,

That is unfortunately the case currently. The MATLAB language interface, unlike most of the other language interfaces in libSBML, are generated by hand rather than generated automatically. It is in our plans to implement 'qual' support this in the near future, but it's not implemented in libSBML now.

We can take a look at how much effort will be required to implement it. Could you let us know how you expect to use it, and what other software (if any) you want to interface with it? This might be useful for us to know what to focus on.

Thanks for your feedback, in any case!

[Sven Thiele]

Hi Michael,

We want to provide SBML-qual support in CellNetAnalyzer. Currently we use
libSBML to parse SBML files. I'd love to avoid writing our own XML parser
in MATLAB. :)

Best regards
Sven

On Fri, Jun 10, 2016 at 1:32 AM, Michael Hucka mhucka@users.sf.net wrote:

Hi Sven,

That is unfortunately the case currently. The MATLAB language interface,
unlike most of the other language interfaces in libSBML, are generated by
hand rather than generated automatically. It is in our plans to implement
'qual' support this in the near future, but it's not implemented in libSBML
now.

We can take a look at how much effort will be required to implement it.
Could you let us know how you expect to use it, and what other software (if
any) you want to interface with it? This might be useful for us to know
what to focus on.

Thanks for your feedback, in any case!

• [libsbml:#425] https://sourceforge.net/p/sbml/libsbml/425/ Missing
  Qualitative Model information*

Status: open
Version: libSBML-5.13.0
Priority:
Created: Wed Jun 08, 2016 01:41 PM UTC by Sven Thiele
Last Updated: Wed Jun 08, 2016 01:41 PM UTC
Owner: nobody

Hello,
I'm using libSBML via the precompiled MATLAB Interface provided here:

https://sourceforge.net/projects/sbml/files/libsbml/5.13.0/stable/MATLAB%20interface/
I want to access the data of qualitative models as detailed in the SBML
QualitativeModels package.
Unfortunately the MATLAB struct created by TranslateSBML() does not
contain any of the data in our SBML files.

regards, Sven

Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/sbml/libsbml/425/

To unsubscribe from further messages, please visit
https://sourceforge.net/auth/subscriptions/

[Sarah Keating]

I know this is probably too late for you; but for the record thr forthcoming release of liBSBML 5.16.0 will include matlab support for the qual and groups packages.