Windows general simulator of metabolic pathways

prm at aber.ac.uk prm at aber.ac.uk
Tue Mar 23 13:53:55 EST 1993


In article <C44w88.557 at sun2.iend.wau.nl> prwiertz at rcl.wau.nl writes:
>
>                                     Wageningen,18-3-93
>
>  I found on an ftp-site a programm wich simulates the metabolic pathways in
>the cell. 

If the program you mention is GEPASI, then it does not simulate _the_
metabolic_pathways_in_the_cell. It simulates metabolic pathways of cells
(both _the_ were intetionally dropped!)

>When yo start the programm nothing is entered, I hope you have not to
>enter all metabolicways yourself. 

Im afraid the answer is YES. (even if the program you mention is a different
one I suspect the answer will be the same)

>Does anyone know where i can find the metabolic pathways. Thanks in advance.
>

look in the EMBL server for a database called ENZYME, but see below

>                                 M.N.G.M. Wiertz
>
>Email:Prwiertz at rcl.wau.nl

I am the author of GEPASI. The philosophy behind the program is that of
trying to be as easy to use as possible, without any knowledge of programming. 
BUT...

it does not have a database with metabolic reactions. You can find an enzyme
database in the EMBL server, but this is _very_ incomplete, for example it
lacks information on kinetic constants, reaction mechanisms, etc. GEPASI 
cannot read this database and I think that due to this incompleteness it would 
be a tremendous effort to make the program read it with very few benefits. I 
am also not interested in creating and maintaining such database, due to 
lack of time.

Having said this, I must say that your question is a relevant one and I will 
take that into consideration for a further version of the program (but don't 
expect too much). Note that such a database would have to take into account 
several different alternative pathways, as many organisms have pathways that 
are different from other (organisms). Indeed it is my opinion that apart from
the energy providing pathways like glycolysis, the TCA cycle, etc. most
organisms have their own speciallized pathways with different enzymes, etc.
Don't belive the metabolic charts we use to devorate the labs. They include
information from sources as far apart as photosythetic bacteria and rats.


For all you lot that have never heard of GEPASI I will post a brief description
of the program.

Pedro Mendes
prm at aber.ac.uk




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