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Dear all,

It has become clear with the success of SBML that we need
also a good representation to communicate *results* of
operations done with models (eg simulation), in a way that
makes those results clearly associated with the model. (The
same applies to experimental data.)

After some considerable brainstorming and lots of
prototyping, we have now created a draft specification for
a Systems Biology Results Markup Language (SBRML). This
draft is now open for comments from the community in the
hope that we will be able to get sufficient feedback to
allow a serious improvement of this specification and be
able to agree (at some SBML forum) to use it as a standard.

We will present this draft at the upcoming SBML Forum, and
open it for discussion there. In the interest of sparing
some trees, we are *not* going to bring hard copies - if
you want to have a hardcopy in Gothenburg, you should print
the PDF in the link below and bring it with you to the
meeting.

The draft document and the corresponding XML schema
definition are available at
http://comp-sys-bio.org/tiki-index.php?page=SBRML
Please have a look!

Joseph Dada, Norman Paton & Pedro Mendes
The Universtity of Manchester

--
Pedro Mendes
Chair in Computational Systems Biology
University of Manchester

School of Computer Science
Manchester Centre for Integrative Systems Biology
131 Princess St., Manchester, M1 7DN, UK
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Dear Pedro,

I welcome the idea of a language for encoding simulation results. Actually,
I think the scope of such a format could be even larger since it could be
used to encode the result of experiments providing results relevant for
dynamical models. After all, the outcome of an experimental timecourse is
not different from the result of a stochastic kinetic simulation. Combining
both could pave the way to a true interface between experiments and
modeling, facilitating model parametrisation and validation.

However, as it is currently, I find that SBRML put a lot of emphasis on the
description of the simulation experiment rather than encoding the results
themself. There is already a community effort in that direction called
SED-ML (formerly MIASE-ML). You can find more information at:
http://www.ebi.ac.uk/compneur-srv/sed-ml/index.html

This language is, I think, being implemented in several software already.
There are maybe some synergy to build here.

Best regards,


Pedro Mendes wrote:
> Dear all,
>
> It has become clear with the success of SBML that we need
> also a good representation to communicate *results* of
> operations done with models (eg simulation), in a way that
> makes those results clearly associated with the model. (The
> same applies to experimental data.)
>
> After some considerable brainstorming and lots of
> prototyping, we have now created a draft specification for
> a Systems Biology Results Markup Language (SBRML). This
> draft is now open for comments from the community in the
> hope that we will be able to get sufficient feedback to
> allow a serious improvement of this specification and be
> able to agree (at some SBML forum) to use it as a standard.
>
> We will present this draft at the upcoming SBML Forum, and
> open it for discussion there. In the interest of sparing
> some trees, we are *not* going to bring hard copies - if
> you want to have a hardcopy in Gothenburg, you should print
> the PDF in the link below and bring it with you to the
> meeting.
>
> The draft document and the corresponding XML schema
> definition are available at
> http://comp-sys-bio.org/tiki-index.php?page=SBRML
> Please have a look!
>
> Joseph Dada, Norman Paton & Pedro Mendes
> The Universtity of Manchester
>

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Dear Nicolas,

> I welcome the idea of a language for encoding simulation results.
> Actually, I think the scope of such a format could be even larger
> since it could be used to encode the result of experiments providing
> results relevant for dynamical models. After all, the outcome of an
> experimental timecourse is not different from the result of a
> stochastic kinetic simulation. Combining both could pave the way to
> a true interface between experiments and modeling, facilitating
> model parametrisation and validation.

This has not escaped us, and we also would like to explore that aspect. Actually, we could have done with a spec like this years ago when we wrote the parameter estimation module of COPASI... So my hope is that this can indeed also serve as a means to encode experimental data in the context of a model.


> However, as it is currently, I find that SBRML put a lot of
> emphasis on the description of the simulation experiment rather
> than encoding the results themself.

It does both. The results are encoded inside the section that describes the operation because we want the results to be directly tied to the operation that produced them. I don't know if you noticed but it has two major ways to encode results: either as tuples or as a hipercube.

> There is already a community effort in that direction called
> SED-ML (formerly MIASE-ML). You can find more information at:
> http://www.ebi.ac.uk/compneur-srv/sed-ml/index.html

We were aware of MIASE and thought that something like that would be the desirable way include to describe the operations. However we opted to make our first draft independent of that, as we did not want to get caught in those discussions at this stage. I hope that it will be easy to adopt SED-ML for the description of operations, like we use SBML for the description of the model. So I think we are all on the same page here and hopefully that is the direction that this will take after the Forum.

Best wishes
Pedro
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