SBML to SBML-qual

[Bill Yang]

Hi everyone,

I am construting some Boolean networks and trying to take the advantage of exisiting SBML models. So I am wondering if there is any SBML to SBML-qual converter available?

Best,

Bill

[Lucian Smith]

A quick search revealed converters from *other* formats to SBML-qual (such as https://academic.oup.com/bioinformatics/article/28/20/2648/207510 for BioPAX, https://lifeware.inria.fr/~soliman/post/casq/ for CellDesigner, and http://www.colomoto.org/software/biolqm.html for other formats), but I don't know of anything that converts SBML-core to SBML-qual.  However, I'm not quite sure what you're after.  Are you hoping to convert SBML-core reactions to SBML-qual transitions?  Or possibly SBML-core events to SBML-qual transitions?  I would have imagined that in both cases, a translator would require more information than was present in the SBML-core model, but perhaps not?

It might be possible to convert your models in a two-step process, such as from SBML-core -> CellDesigner -> SBML-qual.  But I think any success you may have is going to highly depend on how the elements you want translated are currently encoded, and what kind of transformation they'll need.

I'm also copying the colomoto-discuss group in this reply, as they will almost certainly know more.

-Lucian

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