I had a quick look at the paper you mention in science, I havn't read it
thoroghly but what I didn't like on first inspection where the terrible
diagrams attempting to depict the model. I presume the details of the model
are in the supplementary info? One thing we are attempting to do is to build
a model database but sometimes it is very difficult to get hold of models
which are published. In constrast the model you recently published on
glycolsysis was a great example and one others should follow because I was
able to get the model from Pedro's site in SBML and load it into my software
with out any problems at all.
I agree though that the science paper looks better than the nature biotech
paper which was very poor. The people in the science paper have been
modelling for a while and I think they appreciate the problems more than the
authors in the nature biotech paper.
Herbert Sauro
""Douglas Kell"" <dbk at umist.ac.uk> wrote in message
news:3DD67603.10701.20FB6101 at localhost...
> There was criticism in this newsgroup of a model which appeared in
> Nature Biotech in April ("Any one see the april edition of nature
> biotech? There was a modelling paper in the edition. Just wondered
> what people thought. The paper reminded me a great deal of the
> early metabolic models from the 60s, involving hundreds of
> reactions and with very little validation. Also completely devoid of
> theory, I felt it was like subsituting one black box (namely the treal
> thing) for another (a large matlab file).")
>> IMHO a rather more decent one on the NF-kB pathway has
> appeared in Science:
>> The IkB-NF-kB Signaling Module: Temporal Control and Selective
> Gene Activation, by Alexander Hoffmann, Andre Levchenko, Martin
> L. Scott, and David Baltimore, Science 2002 November 8; 298:
> 1241-1245.
>> The supplementary info makes a decent fist of justifying the
> parameters used, discriminating those based on expts (perhaps a
> little coy about the errors involved) from those constrained from
> those 'guessed' by fitting (which still didn't reproduce the data
> perfectly). Is this setting the standards to which cellular/signalling
> modellers should aspire, or do people think there are major things
> that they still should have done before getting a computer model into
> Science?
>> All the best,
> Douglas.
> --
> Douglas Kell,
> RSC/EPSRC Research Chair in Bioanalytical Sciences
> Dept Chemistry, Faraday Building, UMIST, POBox 88,
> Sackville St, MANCHESTER M60 1QD
> Tel: 0161 200 4492 fax: 0161 200 4556 dbk at umist.ac.uk>>> ---
