[sbml-discuss] Need of a Tool Box

Howard M. Salis salis at cems.umn.edu
Wed Sep 22 09:23:11 PDT 2004

Hello Mahesh,

I have been thinking about a similar problem: Given a diagram of some
metabolic or signal transduction pathway or a gene to be expressed, is it
possible to automate the process of deconstructing that diagram into a
system of bio/chemical reactions with all of the accompanying data needed
to simulate the system (ie. kinetic constants, rate laws, diffusivities,
etc). For example, most gene expression may be deconstructed into a
well-conserved system of reactions where most of the kinetics remain
 (more or less) constant from gene to gene. Is this possible for other
biological processes?

Most simulators require the system of reactions to encompass all
significant transitions from one state of the system to another, where the
state is defined by the numbers (or concentration) of all unique
(and important) chemical species. So, the first step would be to define
all the important unique chemical species in the diagram and describe all
of the interactions between each pair of unique chemical species. The
second step may be to quantitatively describe how fast each interaction
takes place, including the rate law (elementary reaction or some sort of
approximate one, like Michaelis Menten) and the kinetic constants. Then
you have to worry about initial conditions.

It'll be a very information-intensive process, but hopefully that
information will be available in the future.

A portion of this problem is mainly a problem of convienance. If you have
all of the information handy, you can always deconstruct the diagram
yourself. But what happens if there's 2000 genes, 400 signalling pathways,
and 15,000 metabolic pathways that you want to model. Even if you had the
information, it would be counter-productive to fully describe the system
by "hand".

-Howard Salis
Dept. Chemical Engineering & Materials Science
University of Minnesota

On Wed, 22 Sep 2004, Mahesh Visvanathan wrote:

> 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,
> Mahesh
> 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
> http://imsb.umit.at

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