23 Mar '11 09:50
The SBML specification for Level 3 Version 1 states that the Trigger element in Events contains the non-optional attributes "persistent" and "initialValue".
I just had a look into the SBML test suite and noticed that some models in Level 3 Version 1 lack the persistent attribute. See, for instance, model 406.
To evaluate the Trigger element, I am using JSBML. This library's getPersistent() method returns false if no persistent attribute has been specified in Level 3. But for previous SBML levels, this method returns true. For these earlier SBML levels, this makes sense, because the behavior of a Trigger was defined as if it had the property persistent=true.
However, I think there are two problems at the moment.
1. The test models seem to be not correct because the persistent
attribute is not optional and has to be present. It seems to be
forgotten in these examples.
2. If this element is forgotten, how should we deal with it? Does the
returned value "false" really make sense? I noticed that the test models
could be simulated with much better quality if I simply set persistent
to true if it was forgotten.
So far, I have never used libSBML, but it would be interesting what the
getPersistent() method in libSBML does in contrast to JSBML.
For myself, I'd like to know what I can assume when dealing with the
missing persistent attribute in Trigger for SBML Level 3.
Wilhelm-Schickard-Institut für Informatik
Lehrstuhl Kognitive Systeme
Tel: (+49/0) 7071 / 29 78987
Fax: (+49/0) 7071 / 29 5091
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