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Metabolic modeling

Pedro Mendes pedro at enzyme.demon.co.uk
Sun Feb 9 17:35:45 EST 1997


In article <Pine.SOL.3.91.970128195540.18829B-100000 at bisance>, bali at citi2.fr 
says...
>
>[...]
>second, you will discover what the word stiff means. because to modelise
>a pathway is equivalent to solve a set of differential equation. 
>The time constant of these ODE are varying in a big order of magnitude.
>[...]

This is a technicality that has been solved since the early 1970s. Any decent 
metabolic modelling program will be able to cope with stiff ODEs. GEPASI, my 
biochemical kinetics simulator (see URL at the bottom of my signature) can 
easily deal with them by using the LSODA solver of ODEs. Other similar
programs are also able to solve stiff ODEs.

Your comment is quite pertinent in the sense that no one can think of writing
a simulator of biochemical kinetics that does not deal with this. But any 
modern simulator can do so. If one wants to simulate biochemical pathways 
one picks one of these programs up and gets on with the business of obtaining 
good estimates for the kinetic parameters (which as you said is a very 
difficult task - by far the biggest obstacle).

-- 
Pedro Mendes
home: pedro at enzyme.demon.co.uk , work: prm at aber.ac.uk | Aberystwyth,
http://gepasi.dbs.aber.ac.uk/pedro/prmhome.htm        | Wales, UK (Eur.Un.)
author of GEPASI http://gepasi.dbs.aber.ac.uk/softw/gepasi.html






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