"Sameer VK" <sameervk.iitkgp@gmail.com> wrote in message
<g1m951$ar$1@fred.mathworks.com>...
> does Simbiology toolbox of Matlab r2007b support SBML level
> 2 and version 3?
Last I checked SimBiology supported portions of SMBL Level 2 version 1.
(Yeah, thats a few versions behind...)
I bought SimBiology thinking it'd be a convenient GUI environment to use to
convert my models into SMBL-format for some journals that are starting to
require such versions.
I found it to be clunky and limited in the SBML features it supported. Further,
the Export to SBML function generates an XML file that is as horrendously
coded as any code you'd get from saving an MS Word file as HTML. I had to
go back and manually edit the file so I wouldn't feel embarrassed when a
fellow modeler looked at it.
Don't buy SimBiology if you want to use it for SBML conversion or for
importing SBML-encoded models from the BioModelsDatabase. SBML support
in this product seems like it was more of an after-thought by the developers.
If you go up to sbml.org you can get an open-source SBML toolbox for
MATLAB. It may not be as pretty as SimBiology, but at least it supports SBML.
"Jeff " <jkear_REMOVE_ns@ucsd.edu> wrote in message
<g1mt2h$1fp$1@fred.mathworks.com>...
> "Sameer VK" <sameervk.iitkgp@gmail.com> wrote in message
> <g1m951$ar$1@fred.mathworks.com>...
> > does Simbiology toolbox of Matlab r2007b support SBML level
> > 2 and version 3?
>
> Last I checked SimBiology supported portions of SMBL Level
2 version 1.
> (Yeah, thats a few versions behind...)
>
>
> I bought SimBiology thinking it'd be a convenient GUI
environment to use to
> convert my models into SMBL-format for some journals that
are starting to
> require such versions.
>
> I found it to be clunky and limited in the SBML features
it supported. Further,
> the Export to SBML function generates an XML file that is
as horrendously
> coded as any code you'd get from saving an MS Word file as
HTML. I had to
> go back and manually edit the file so I wouldn't feel
embarrassed when a
> fellow modeler looked at it.
>
> Don't buy SimBiology if you want to use it for SBML
conversion or for
> importing SBML-encoded models from the BioModelsDatabase.
SBML support
> in this product seems like it was more of an after-thought
by the developers.
>
> If you go up to sbml.org you can get an open-source SBML
toolbox for
> MATLAB. It may not be as pretty as SimBiology, but at
least it supports SBML.
I'm trying to use Optimization toolbox to analyse
biochemical pathways, for that I need to import SBML file to
obtain the stoichiometric matrix, what softwares do I need
to install to import SBML file into matlab and get the
matrix as ana M-file?
Tags for this Thread
Add a New Tag:
Separated by commas
Ex.: root locus, bode
What are tags?
A tag is like a keyword or category label associated with each thread. Tags make it easier for you to find threads of interest.
Anyone can tag a thread. Tags are public and visible to everyone.
NOTICE: Any content you submit to MATLAB Central, including personal information, is not subject to the protections which may be afforded information collected under other sections of The MathWorks, Inc. Web site. You are entirely responsible for
all content that you upload, post, e-mail, transmit or otherwise make available via MATLAB Central. The MathWorks does not control the content posted by visitors to MATLAB Central and, does not guarantee the accuracy, integrity, or quality of such content.
Under no circumstances will The MathWorks be liable in any way for any content not authored by The MathWorks, or any loss or damage of any kind incurred as a result of the use of any content posted, e-mailed, transmitted or otherwise made available
via MATLAB Central.
Read the complete Disclaimer prior to use.
Feed for this Thread
E-mail this page to a colleague