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[cellml-discussion] ABI CellML meeting minutes 2009-09-30


Chronological Thread 
  • From: david.nickerson at gmail.com (David Nickerson)
  • Subject: [cellml-discussion] ABI CellML meeting minutes 2009-09-30
  • Date: Tue, 27 Oct 2009 11:23:17 +1300
> I cc:ed Ion as I must confess I didn't follow developments on VCell neither.
> Maybe he could state on how things evolved.
>
> Additionally, Richard Adams at Edinburgh University did some work on Java
> library development for SED-ML.
> It is all at:
> http://miase.svn.sourceforge.net/viewvc/miase/sed-ml/jlibsedml/
> There also is an online SED-ML file validator at:
> http://www.bioinformatics.ed.ac.uk:8080/SBSVisualWebApp/html/sedml/
> Richard said, it is all still preliminary, but we were discussing on
> continuing the development,
> so maybe it would be a good idea to get in contact with him - so as not to
> do things twice...
> I also cc:ed Richard :-)

thanks Dagmar (and Richard for the correction), if I get a chance I'll
be having a look - although my Java is not particularly strong.

> SED-ML would allow you [being in Auckland] to send me [being in Rostock] the
> *description* of what you did, so that I can launch a simulation tool and
> repeat the steps you did.
> If you want to reuse the simulation data ("results"), you probably want to
> use efforts such as SBRML from Pedro Mendes' group to do so
> (http://www.comp-sys-bio.org/tiki-index.php?page=SBRML).
> You could include a reference to a result data set encoded in SBRML in your
> SED-ML file (as a note only, currently) to refer to the result data from
> your simulation description.
> ... if that is what you want ... :-)

yep. it will certainly be interesting to see how this evolves -
whether people actually want to share results or if you always want to
re-run the simulation in your own tool :)


Cheers,
Andre.


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