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From: jo bruck on 4 Apr 2008 10:57
Can only add my experience and cry for help:
After I managed to use SimBiology to manipulate an existing
SBML model (Teusink(a)al from JWS database) and exported the
results into SBML, neider COPASI nor CellDesigner nor (the
less famous)SBML-PET could read my file, while they don't
have problems with the original one... Weeks of work for
nothing...

....unless someone knows what are the allowed 'moves' in
SimBiology which result in a model which, when exported, can
be read into those sofwares.

Whether this is the same version issue which Jeff complains
about, or SimBio creates some invalid code, I do not know.

thx for comments!

"Jeff " <jkear_REMOVE_ns(a)ucsd.edu> wrote in message
<favco5$6rc$1(a)fred.mathworks.com>...
> Does anyone know how update the export to SBML feature in
SimBiology?
>
> Simbiology can currently export SBML files that contains
*some* of the SBML 2.1
> features (released 6/2003) and has no support for v2.2
(9/2006) or v2.3
> (6/2007).

> Does 2007b update the SBML compatibility? If not,
Mathworks marketing
> department should really remove the "Export to SBML" item
on the SimBiology
> feature list. If you bought a program that claims to
export to MS Word format
> you would be upset if it only supported some parts of the
Word 97 format and
> no support for more recent versions.

From: EL on 4 Apr 2008 12:41
jo bruck schrieb:

> Can only add my experience and cry for help:
> After I managed to use SimBiology to manipulate an existing
> SBML model (Teusink(a)al from JWS database) and exported the
> results into SBML, neider COPASI nor CellDesigner nor (the
> less famous)SBML-PET could read my file, while they don't
> have problems with the original one... Weeks of work for
> nothing...

Which version of SimBiology do you use? 2.2 in 2007b+ has improved SBML
(v2.1) support.
Another question: why do you want to open it in COPASY or CellDesigner?
Is there anything you can not do with SimBiology but like to do?


Eckhard
From: jo bruck on 8 Apr 2008 10:37
Thanks for the quick answer!
>
> Which version of SimBiology do you use? 2.2 in 2007b+ has
improved SBML (v2.1) support.

Right, I have only 2007a...

> Another question: why do you want to open it in COPASY or
>CellDesigner? Is there anything you can not do with
SimBiology but like to do?

well...two answers.
1.sure, you usually want to be able to use more than one
tool. In this case, as far as I know, Matlab is way too slow
to do parameter scan/fit (I have 20 ODEs and up to 100
parameters, no, I wont fit all of them) since numerical
integration does not happen within a compiled code.(I assume
most tools allowing parameter fit convert stuff in
C/fortran/whatever) While I am far from being able to make
sound suggestions, I am wondering why a compiled C code
cannot be produced with Matlab. (or write a C-integrator and
include as MEX?)
This slow speed is exactly the reason, why my group did not
buy a newer version of SimBiology.

2. may I remind you that a main reason of having a common
standard is that it is common. We want to share the results
with our friends/collegues (who will then cite us). E.g. I
have started with downloading a SBML modell the author of
which I will cite... That's why I chose a tool able to
communicate in SBML in the first place. only its not, so I
guess I will have to try http://sbml.org/Software/SBMLToolbox
no money but endless hours of intallation sessions involved...
From: jo bruck on 9 Apr 2008 09:50
> tool. In this case, as far as I know, Matlab is way too slow
> to do parameter scan/fit (I have 20 ODEs and up to 100
> parameters, no, I wont fit all of them) since numerical
> integration does not happen within a compiled code.(I
assume most tools allowing parameter fit convert stuff in
> C/fortran/whatever) While I am far from being able to make
> sound suggestions, I am wondering why a compiled C code
> cannot be produced with Matlab.

Comment on my previous:
Hennings Schmidt's SBtoolbox2 + SBPD (add-on), based on
'SBMLtoolbox' and 'libSBML') might be a serious Matlab tool
too, I am still in the making friends phase though.
AND he seems to have dealt with the above speed issue:
(under "High Performance Simulation")
http://sbtoolbox2.org/main.php?display=documentationSBPD&menu=overview

According to the website, for exporting files, all but one
SBML Vers.2 features have been implemented.
(if it also accepted SimBio code, this would be an answer
to the topic creator's question...:(


From: jo bruck on 9 Apr 2008 09:50
> tool. In this case, as far as I know, Matlab is way too slow
> to do parameter scan/fit (I have 20 ODEs and up to 100
> parameters, no, I wont fit all of them) since numerical
> integration does not happen within a compiled code.(I
assume most tools allowing parameter fit convert stuff in
> C/fortran/whatever) While I am far from being able to make
> sound suggestions, I am wondering why a compiled C code
> cannot be produced with Matlab.

Comment on my previous:
Hennings Schmidt's SBtoolbox2 + SBPD (add-on), based on
'SBMLtoolbox' and 'libSBML') might be a serious Matlab tool
too, I am still in the making friends phase though.
AND he seems to have dealt with the above speed issue:
(under "High Performance Simulation")
http://sbtoolbox2.org/main.php?display=documentationSBPD&menu=overview

According to the website, for exporting files, all but one
SBML Vers.2 features have been implemented.
(if it also accepted SimBio code, this would be an answer
to the topic creator's question...:(


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