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.ad...@ed.ac.uk
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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