Chronological Thread 

< Chronological >      < Thread >

---

Dear all,

I would like to add to Nicolas' comments that we have put a SED-ML
sample file specifying the simulation of a biochemical model (in this
case indeed an SBML model - BIOMODELS 21) in the sourceforge SVN
repository of the MIASE project.
I hope it gives you a better idea of the SED-ML format that encodes the
MIASE guidelines:
http://miase.svn.sourceforge.net/viewvc/miase/sed-ml/examples/

A detailed description of both the above SED-ML example and the SED-ML
format itself is also available from:
http://miase.svn.sourceforge.net/viewvc/miase/sed-ml/documents/
You might want to have a look at the provided paper in order to
understand our idea of the format (section 2) and go through the
explanation of the XML example (section 3). The paper has been submitted
to and is going to be published after the CMSB 2008 conference.


I agree with everything Nicolas already said in his last mail and would
really appreciate your comments on the format, especially your doubts
concerning the closeness to SBML.

Thanks for your interest in MIASE/SED-ML.
Dagmar


Nicolas Le nov?re wrote:
> Some comments from Big Brother ;-)
>
> "# We don't really have a good idea of this, but Andrew mentioned MIASE,
> which is apparently supposed to be format agnostic, but appears to be quite
> specific to SBML so far"
>
> Why is-that? As far as I know, there is nothing in SED-ML (the new name of
> the format that try to implement some of MIASE support) that is specific to
> SBML. If you disagree, we would be happy to get in touch to solve that.
> SED-ML is really meant to be entirely format independent ... as far as the
> format is some kind of XML, since the variable are targeted using XPATH
> (and even that could be argued, since an XPATH can be transform into any
> kind of pointer)
>
> "# When they distributed their specification initially, Andrew was
> concerned about their assumption that time be the only x-axis value
> possible. They did not make any response to his comments. "
>
> Probably because we overlooked the comment. It is of course not true. Any
> dataGenerator can be used on x, y or z.
>
>
> "MIASE also lumps graphing and simulation together, which we do not believe
> to be appropriate for CellML"
>
> Yes ... and no. SED-ML says what to plot against what. Not how (except for
> the linear vs log).
>
> "# We should keep an eye on MIASE and see how it develops. Poul doesn't
> think it is worth making our graphing and simulation metadata
> MIASE-compliant unless the standard has a significant following"
>
> I completely understand that. We are currently aware of five
> implementations under way, by COPASI, VCell, BioUML, SBToolBox and SBW.
>
> But I think there is a slight misunderstanding here, that is entirely our
> fault. Initially well separated, the MI and the format tended to blur
> around the new year. We are doing our best to more cleanly separate both.
> SED-ML is akin to SBML and CellML. MIASE is akin to MIAME. CellML does not
> have to implement SED-ML. This is the job of the simulation software.
> SED-ML will call CellML and SBML models and describe what to do with them.
>
> MIASE is another issue. It is meant to describe the minimal information to
> encode in order to reproduce a simulation. CellML graphing and simulation
> metadata are/will be MIASE compliant. Otherwise they are not sufficient.
>
> But in fact MIASE is for the moment just an idea. And we will be in touch
> with everyone in order to formalise it more, and transform it into a
> "MIBBI-grade" checklist (MIBBI is the portal that federates the MIs.
> Publication to appear inn Nat Biotech next week)
>
> Cheers,
>
> James Lawson wrote:
>
>> Dear CellML community,
>>
>> The ABI CellML team meeting minutes for last Wednesday (2008-07-30) are
>> now available at:
>> http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2008-07-30/
>>
>> Kind regards,
>> James Lawson
>>
>> _______________________________________________
>> cellml-discussion mailing list
>> cellml-discussion at cellml.org
>> http://www.cellml.org/mailman/listinfo/cellml-discussion
>>
>
> _______________________________________________
> cellml-discussion mailing list
> cellml-discussion at cellml.org
> http://www.cellml.org/mailman/listinfo/cellml-discussion
>

---

• [cellml-discussion] ABI CellML team meeting minutes 2008-07-30, James Lawson, 08/05/2008
  • [cellml-discussion] ABI CellML team meeting minutes 2008-07-30, Nicolas Le novère, 08/06/2008
    • [cellml-discussion] ABI CellML team meeting minutes 2008-07-30, Dagmar Köhn, 08/08/2008

---

Archive powered by MHonArc 2.6.18.