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From: Henning Schmidt on 11 Apr 2008 02:10
SBML and its support:

Yes, this is totally right. Although SBML is termed a "standard" for the representation of biochemical systems there is NO SINGLE (SIMULATION) TOOL on earth that does support ALL the features of SBML. Most don't even support all features of the old Level 1 Version 2 specification!

BUT all developers work hard on it!

Note that sometime after summer an SBML test suite will be available from the SBML Team. This test suite can be used to test the SBML implementation in a given tool against thousands of examples. Developers can run the testenvironment and upload the results, which probably will be published on sbml.org.

The nice thing is that users of tools can rerun the tests ... and check for themselves.

This will be a major step in the documentation of which tools support what and if they do it correctly. So users can select the tool that supports the features they require for their modelling work.

HS
From: Ricardo Paxson on 11 Apr 2008 08:31
"Ricardo Paxson" <pax(a)remove.this.mathworks.com> wrote in message
<ftm7mb$5fm$1(a)fred.mathworks.com>...
> Hello,
>
> There are 3 different topics being discussed here, 1) SBML compliance, 2)
Analysis methods and 3) Simulation Performance. I
> would like to add some info on each:
>
> 1) SBML compliance is a difficult matter. While it is meant to be a standard
format, we have not seen any tool, commercial or
> open-source, that supports the entire specification. SimBiology supports
most of the standard but not all of it; we are working to
> close this gap. I might add that supporting Unit specifications, which
SimBiology does, adds a fair amount of complication to this
> matter since the format has changed a couple of times in incompatible
ways, e.g. SpatialSizeUnits.
>
> 2) There are a variety of analysis methods needed by modelers. SimBiology
has many of these (see
> http://www.mathworks.com/products/simbiology for more info.) and of
course we are working on more. Our process is to
> prioritize features requested by users so if you have specific needs please
let us know.
>

Another point to add here is that SimBiology, like SBTOOLBOX2, is written in
MATLAB. This makes extending the functionality of SimBiology with user
written scripts a simple matter.

> 3) SimBiology simulation performance has been essentially MATLAB's ODE
performance since version 1.0. We are aware that for
> large models this is not adequate. A straightforward approach to increasing
simulation performance is to generate C/Fortran code
> from MATLAB code and compile it on the fly (meaning without requiring the
user to do anything). There are a few ways to do this
> in MATLAB; one of them is the MEX interface as mentioned in a previous
post. SimBiology is likely to do something similar in the
> near future.
> In the meantime there are 2 things that might help. In the version of
SimBiology that shipped with R2008a we have added a third
> party solver implemented in C; this adds some performance for a class of
models.
> And secondly, for problems such as parameter scans (where each run is
independent of the others), the use of the Parallel
> Computing Toolbox in conjunction with SimBiology increases performance
proportionally with the size of the cluster.
>
> On a separate note, I have emailed people on this thread asking for
information on which features of SBML where being used by
> the model that did not work, but I have not heard back. If someone could
post what the troubles are with SBML import/export we
> would very much appreciate it.

I would like to clarify this last sentence. I would be interested in learning what
features of SBML are used by the model in this post.

>
> Cheers,
>
> -pax
>
>

-pax


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