[BiO BB] cell simulation

Gary Bader bader at cbio.mskcc.org
Mon Oct 13 12:49:56 EDT 2003


Hi Deepan,

> -----Original Message-----
> From: bio_bulletin_board-admin at bioinformatics.org
> [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of deepan
> chakravarthy n
> Sent: Monday, October 13, 2003 11:58 AM
> To: bio_bulletin_board at bioinformatics.org
> Subject: [BiO BB] cell simulation
> 
> hello ,
>       i  am  writing algorithm for a cell simulation
> software.
> 
> 1)
> we know  complex reactions are involved in cell
> metabolism.
> many reversible rxns, non reversible rxns are
> involved.
> to calculate the concentration of each  component at a
> given instant we have to use complex differential
> equations.
> if someone can suggest me some websites or books to
> refer for such calculations plz do it.

Many software tools are available for these calculations.  Some of these are
open source, so you can see how the calculations are done.  See
http://sbml.org for more details.

> 2)
> i have taken  my reference cell as E.Coli . where can
> i get the complete set of metabolism rxn involved  in
> EColi .(along with
> the values of equlibrium constants)
> 

The best resource for E.coli pathways is EcoCyc: http://www.ecocyc.org/  But
other resources exist for simulation e.g.
http://gcrg.ucsd.edu/organisms/ecoli.html for flux-balance based
simulations.

> plese guide me if possible
> 
> 
> 
> =====
> ---------------------------------------------
> deepan chakravarthy n
> 2nd year,(2nd sem),
> b.tech(biotech),
> anna university ,
> chennai.
> ph no:
> hostel:22354862(044)room no205,
> home:04287-241199,04287244399,
> address:
>  ac tech hostel (jh 207),
>  anna university,
>  chennai-25.
> 
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