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April 2007
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Posts: 170
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December 2006
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Re: species and reactions outside of models
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04 May '07 06:47
 
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Hello Daniel,
The simple answer is no it is not possible to define reactions and
other objects outside a model. In chapter 4.1 of the SBML specifications
it says that the top level of an SBML file is the the SBML container
which must include exactly one Model element. I hope that helps.
Thanks,
Stefan
On Thu, 03 May 2007 03:42:50 -0700 (PDT)
Daniel Primaveßy <s9daprim@stud.uni-saarland.de> wrote:
>
> Hello,
>
> I have a question: Is it possible to define species or reaction
> objects outside of models? All examples in the documentation are
> defined within a model. Probably I overlooked something, but I can't
> find a hint that it isn't possible to define them outside of one.
>
> ____________________________________________________________
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>
> For questions or feedback about the sbml-discuss list,
> contact sbml-team@caltech.edu.
--
Stefan Hoops, Ph.D.
Senior Project Associate
Virginia Bioinformatics Institute - 0477
Virginia Tech
Bioinformatics Facility I
Blacksburg, Va 24061, USA
Phone: (540) 231-1799
Fax: (540) 231-2606
Email: shoops@vbi.vt.edu
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Posts: 961
Registered:
October 2003
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Posts: 3
Registered:
April 2007
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Posts: 469
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October 2003
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Re: species and reactions outside of models
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04 May '07 22:47
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> Of course. I'm writing a PlugIn to export pathways and their topologies to
> SBML and BioPAX. BioPAX isn't a problem at all, but for SBML my idea was
> to map all kind of molecules to the Species class, all kind of reactions
> to the Reaction class and all kind of Pathways to the model class.
> This works perfectly if I have just one pathway to export, but if I have a
> reaction or a molecule that is not part of a pathway I would need to
> export it outside of a model.
It is not part of a pathway, but it is still part of a compartment, isn't it?
> If I had more than one pathway to export I
> would need to write more than one model class.
And what if a species belongs to several pathways? Would-you write several
species representing the same pool?
I think in your case, you need to write down different models (therefore
different SBML file in L2V3). Just take care of the annotations of species
and compartments, so that merging is easy afterward.
But it also boils down to the fact that SBML is not a format to represent
Pathways ...
(that says, all your issues: groupings, tagging, model composition etc.
have been discussed in the past, and will be again. I encourage you to
saty in touch and participate to the development of SBML Level 3)
--
Nicolas LE NOVERE, Computational Neurobiology,
EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Tel: +44(0)1223494521, Fax: +44(0)1223494468, Mob: +44(0)7833147074
http://www.ebi.ac.uk/~lenov, AIM:nlenovere, MSN:nlenovere@hotmail.com
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Posts: 3
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