[sbml-discuss] Need of a Tool Box

Syed Asad Rahman asad.rahman at uni-koeln.de
Wed Sep 22 13:33:33 PDT 2004

Dear Mahesh,

One way can be to find k-shortest path between a substrate and product using
"pathway hunter tool" (http://www.pht.uni-koeln.de).

This tool can be used for automated reconstruction of metabolic pathways and
visualization of the same.

This tool further provides the reaction and enzymes involved during the
conversion and a "stoichiometric matrix" for the model, which can be used
for further analysis like simulation.

Best regards,


S. Asad Rahman, BioInformatician 
CUBIC, Zuelpicher Str. 47, 50674 
Koeln (Cologne), Germany 
Home page: http://www.cubic.uni-koeln.de/personnel/rahman.htm
Email: asad.rahman at uni-koeln.de 
Phone: +49-221-470-7719(O),+49-221-2978686(R) 
FAX :  +49-221-470-5092

-----Original Message-----
From: sbml-discuss-bounces at caltech.edu
[mailto:sbml-discuss-bounces at caltech.edu] On Behalf Of Mahesh Visvanathan
Sent: Wednesday, September 22, 2004 11:27 AM
To: sbml-discuss at caltech.edu
Subject: [sbml-discuss] Need of a Tool Box

Dear All,
  I am looking for a tool box through which we can derive reaction equations
from  a given set of component equations or vice versa for a particular bio
kinetic  network model.
Currently the tool boxes that are avilable in SBML website perform
simulations based on a set of reaction equations for different pathways. But
there are some pathway models where in you have  component equations
avilable in the literature and if we want to implement and oberve these
models using the tools specified in SBML website it is not possible.Because
most of the tool boxes allow simulation based on  reaction equations. 
 Hence for this reason I am looking for a tool box wherein we can derive a
set of reaction equations from a given set of componet equations for a
particular pathway model. Then based on these equations we could perform
simulations and sensitivity analysis for different pathways.
We are much interested to know if any one has come across this kind of
problem. Did any were able to solve this problem based on any toolbox in
matlab or in any other environemt. If any tool box is avilable and if it can
be shared or any sugesstion is kindly welcomed.
 I am egarly awaitng the  positive response from our research community.

Thaking you all,
with regards,

Mit freundlichen Grüßen/
Best Regards,
Mahesh Visvanathan
Research Assistant
Institute for Biomedical Signal  Processing and Imaging
University for Health Sciences, Medical Informatics and Technology
Innrain 98, 6020 Innsbruck, Austria
Tel: +43-50-8648 3851
Fax: +43-50-8648 3850
mahesh.visvanathan at umit.at 

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