Chronological Thread 

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Hi Dagmar, Andre, all:

On VCell side, there is nothing new since August, as we have been tied up
with a few major grant submissions (last one, and biggest one, went out the
door yesterday...)

We did complete in early summer the pure Java library to handle SED-ML
elements, as I mentioned in Auckland that we would... The link to the VCell
solver is also done, but has the obvious limitations of SBML/VCML
incompatibilities. (btw, a lot of these should go away soon due to a
parallel development effort)

I'm not sure whether the library has been updated to match the latest changes
in SED-ML over the summer, and whether it was posted to our Wiki or
elsewhere. I am cc'ing Dan, who is the main MIASE-related developer on our
team, and should be able to give more detailed answers.

Ion

________________________________________
From: Dagmar Koehn [dagmar.koehn at uni-rostock.de]
Sent: Monday, October 26, 2009 6:44 AM
To: CellML Discussion List
Cc: Moraru,Ion; Richard Adams
Subject: Re: [cellml-discussion] ABI CellML meeting minutes 2009-09-30

Hej Dandre :-),

some statements inline.

David Nickerson wrote:
> Hi Dagmar,
>
> Thanks for your comments! I'll just make a couple of notes inline below...
>
>
>> * Andre said that SED-ML does not yet support everything that we
>> need to do for simulation and graphing.
>>
>> I agree that SED-ML still is at quite an early stage and might not cover
>> everything needed.
>> However, even if the structure of SED-ML does not offer particular
>> constructs for some of your needs, you are allowed (by definition of the
>> SED-ML schema) to attach annotations to *any* SED-ML element. Thus, you
>> could "extend" SED-ML towards supporting whatever additional needs you
>> might
>> have for information to put in the simulation description file.
>> Do you think that would be sufficient? As Nicolas mentioned, that would
>> actually be a nice benchmark for us to see in what way SED-ML needs to be
>> extended (certainly by what you would put in the annotations often).
>>
>
> I agree. The way forward here is to start using SED-ML with CellML
> models and see how things work out and what possible extensions are
> required, and also whether these can be incorporated through the
> existing annotation mechanism. I know that at least myself and maybe
> others have volunteered to do this at some point, but I have yet to
> sit down and do it :) We are also hoping that a core SED-ML supporting
> library or tool might become available that we could work with in
> order to implement support for CellML. From the Waiheke meeting, Ion
> offered to make the VCell code available but I haven't had a chance to
> follow up on this.
>

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 :-)

>> * Andrew said that we are still trying to convince the SED-ML group
>> to separate out graphing and simulation.
>>
>> I can say that SED-ML is *not* about graphing at all - in the sense that I
>> understand graphing. SED-ML should provide the description of the data that
>> is used to create the output, and also how these data relate, e.g. for a 2
>> dimensional plot you would have to specify what to plot against what (x and
>> y axes). Let me cite Nicolas again from an earlier mail: "E.g. we can
>> create
>> a report {time, var1, var2}, but some information will only emerge if we
>> "plot" var1 versus var2. In some sense the relationship between var1 and
>> var2 representation is part of the post-processing."
>>
>
>
>
>> * Andre said that you might want to change some of the graphing
>> metadata to get different graphs from the same simulation, or vice
>> versa.
>>
>> If we are talking about running one simulation and creating a number of
>> different graphs (say, many 2D plots) from that simulation, this is already
>> possible in SED-ML right now. All you have to do is to define a number of
>> (what we call) data generators, referring to the variables/parameters you
>> want to use for your output. Then you can define as many outputs as you
>> want, referring to the same or different data generators and to the same of
>> different simulation setups.
>> If you look at the example given in the publication of CMSB 2008, on page
>> 9/10 (http://www.springerlink.com/content/n67n137071431xt7/), we defined a
>> data generator called "time" and we use it to create 2 different curves
>> from
>> one single simulation (only the x axis is varying here, using 2 different
>> models).
>>
>> If we, however, are talking about producing the same graph one time with a
>> red line, one time with a green line - those things are not part of SED-ML
>> core information, and they should go to the above mentioned annotations.
>>
>
> no, what this is addressing that modellers should be able to reuse
> different parts of the simulation experiment description without
> needing to redefine it. For example, here in Auckland I define an
> experiment using the Hodgkin-Huxley model with a certain stimulus
> protocol and produce some action potentials. Now you over in Rostock
> want to use that data to produce some current-voltage data. It would
> be great if you were able to make use of my simulation description and
> its resultant data without having to redefine the simulation
> description locally or perhaps even re-running the simulation. I'm not
> sure if this is already something that SED-ML can include, but it is
> certainly something that we'd be keen to see in the future.
>

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 ... :-)

Best,
Dagmar

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• [cellml-discussion] ABI CellML meeting minutes 2009-09-30, Dougal Cowan, 10/06/2009
  • <Possible follow-up(s)>
  • [cellml-discussion] ABI CellML meeting minutes 2009-09-30, Dougal Cowan, 10/08/2009
    • [cellml-discussion] ABI CellML meeting minutes 2009-10-07, Alan Garny, 10/08/2009
    • [cellml-discussion] ABI CellML meeting minutes 2009-09-30, Dagmar Koehn, 10/09/2009
      • [cellml-discussion] ABI CellML meeting minutes 2009-09-30, David Nickerson, 10/13/2009
        • [cellml-discussion] ABI CellML meeting minutes 2009-09-30, Dagmar Koehn, 10/26/2009
          • [cellml-discussion] ABI CellML meeting minutes 2009-09-30, Richard Adams, 10/27/2009
          • [cellml-discussion] ABI CellML meeting minutes 2009-09-30, David Nickerson, 10/27/2009
          • [cellml-discussion] ABI CellML meeting minutes 2009-09-30, Moraru,Ion, 10/28/2009
  • [cellml-discussion] ABI CellML meeting minutes 2009-09-30, Peter Hunter, 10/09/2009

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