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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.

> ? * 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."

related to the point below, but what I think this is hinting at is
that we prefer to see a distinction between describing and performing
a simulation and processing/extracting/manipulating/graphing the
resultant data. I don't see this as a major sticking point at present
but rather something that will evolve over time if we can get the SBML
and CellML communities using a common simulation experiment
description framework.

> ? * 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.

In terms of actually defining the presentation of specific outputs
(lines on a graph, surfaces, points, etc), this again is something
that we are very keen on in order to be able to unambiguously and
completely describe outputs from a simulation experiment. This is not
a small problem, although the current CellML graphing metadata begins
to address this in regard to specific types of outputs. As above, we
don't see this as a major issue blocking the adoption of SED-ML for
use with CellML models, more something that will come out of this work
if required by the communities. And would most likely fit into the
existing annotation framework.

> ? * Peter said that we want to encourage cooperation, and use accepted
> ? ? standards if they exist.
>
> I cannot tell you how much we would like to see CellML using SED-ML :-)
> I know that we do progress pretty slowly, and I am very sorry for that.

yep, and progress this end is just as slow. I'm not sure if any of the
core SED-ML group are planning to attend the CellML workshop in
February next year, but it would be useful I think to get people
together at some conference or other and see if we can work through
some concrete examples. I'll be at the INCF workshop in Bangalore next
month and I think Nicolas will also be there (along with Jim from the
Virtual Cell?), so hopefully we'll get a brief chance to talk about
SED-ML over those few days...


Thanks again for your comments :) and to follow-up Peter's reply, we
are certainly keen to start trying out SED-ML...just need to find the
time...


Cheers,
Andre.

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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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