[sbml-qual] first published qual model? :)

[Tomas H. <the...@un...>]

Hi All,

Our paper with a comprehensive, multi-scale model of signal transduction 
in human mammary epithelial cells just appeared online: 
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0061757

Of course the model is published with the paper in our SBML qual format :)

Tomas


-- 
----
Tomas Helikar, Ph.D.
Department of Mathematics, DSC 241A
University of Nebraska at Omaha
e: the...@un...
t: 402-554-3999
w: http://mathbio.unomaha.edu;
    http://www.thecellcollective.org

On 04/15/2013 09:19 AM, Chris J. Myers wrote:
> Hi,
>
> I've read over the changes, and I think my concerns have been addressed.
>>
>> One point (made by Lucian) that we were unable to address, was the fact
>> that some attributes have different interpretations depending on whether
>> the model is a logical model or a Petri net model. This is actually a
>> "feature" of the spec given it facilitates the use of the same syntax to
>> define either class of model. Hopefully we have clarified everything so
>> these differences make sense :-)
>>
> Lucian may have a different impression, but I think this sentence has 
> addressed my concern in this regard:
>
> The attribute is not required and even if 25 explicitly stated, the 
> restriction imposed by place capacities in a Petri net model must be 
> encapsulated within the 26 math element of the FunctionTerm elements.
>
> My interpretation of this sentence is that it includes our agreement 
> which was that Petri net models that want to enforce capacity have to 
> put it in their function terms.  The maxLevel is not used to enforce 
> it.  This seems a reasonable compromise, and cleans up the most 
> significant semantics problem.  If I'm misinterpreting this sentence, 
> please let me know.
>
> Thanks to all those who worked hard on getting this specification to 
> this "final" stage.
>
> Cheers,
>
> Chris
>
>
>
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