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


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  • From: radams at staffmail.ed.ac.uk (Richard Adams)
  • Subject: [cellml-discussion] ABI CellML meeting minutes 2009-09-30
  • Date: Mon, 26 Oct 2009 11:37:13 +0000

Hi Dagar,
The validator link is actually:

http://www.bioinformatics.ed.ac.uk:8080/SBSIWeb/html/sedml/

Best wishes
Richard

> 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



--
Dr Richard Adams
Senior Software Developer,
Computational Systems Biology Group,
University of Edinburgh
Tel: 0131 650 8285
email : richard.adams at ed.ac.uk

--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.




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