Thanks Dagmar. We are committed to SED-ML! Your comments are very helpful. Peter
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----- Original Message -----
To: CellML Discussion List <>
Sent: Fri Oct 09 19:41:19 2009
Subject: Re: [cellml-discussion] ABI CellML meeting minutes 2009-09-30

Dear all,

I'd like to comment on the last meeting minutes, particularly on the 
metadata specification comments made by Andre:

    * 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).

    * 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 

    * Andre said that you might want to change some of the graphing
      metadata to get different graphs from the same simulation, or vice

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 (, 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 

    * 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.

    * Andre said that the minimal information standard should be out soon.

Maybe a word on that: We are currently (and have been for a while... 
slow again, I know) working on writing up the MIASE guidelines. In my 
opinion, we do make good progress and I think that we have come to quite 
a good consensus already. So, there is hope that "soon" won't take too long.

I am happy to answer all the questions you might have!

Many greetings from Rostock,

Dougal Cowan wrote:
> I have put the minutes from this Wednesday's meeting up at:
> Dougal
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