Pedro, thanks a bunch for your response.
>Oh, but there are a lot more. Just as an example, I got these out of my
>bibliographic database:
I have some of these but not all of them. Pubmed seams hopelessly
ineffective at turning them up, what do you think is the best resource
for literature searches in these field> 1. I am curious to read what
people think of as the legacy of this?
>I don't think it is true that the number of papers on simulators is
larger
>than on simulations. For example, my own program Gepasi has a list of
>around 50 papers that have used it for research. You can see this list
at
>http://www.gepasi.org (follow the link "Gepasi in research".) The same
>happens with Scamp, although I don't think that Herbert has compiled
such a
>list.
I looked at this list some time ago. It seams as if most of the papers
involve simulations of individual reactions/enzymes (though there are
exceptions). Can you give me some idea of how Gepasi used in this
context, and/or maybe identify one or two of the papers as the good
exemplars of said use?
>Incidentally, I think that the bioinformatics community is (or should
be)
>somewhat well aware of this area. If nothing else, most modern
simulators
>(eg Scamp, Gepasi, MeraModel, MIST) were published in the journal that
is
>now called Bioinformatics!
You might be suprised at the degree of understanding of many
bioinformatics practioners about simulation work. I may just be
projecting my own initial misperceptions, but I think people in many
informatics communities don't appreciate the difficulty of kinetic
modeling, and in particular the challenges of kinetic data which, unlike
the genomic data we are used to trafficking, is expensive to obtain,
highly sensitive to experimental condition, difficult to evaluate in
vivo, and of limitted use outside of the particular model for which it
is gathered. Most people in informatics that I've talked to believe
that the way one would do a simulation of a metabolic pathway is by
writing a computer program to pull down Km and Kcat values from some big
database like BRENDA and plugging them into a simulation engine.
>But I guess that a review will not harm anyone
>here, as long as you manage to portrait the field with accuracy.
I am writing the review partly to educate myself about the field (as you
can see, I need a lot of education!) and partly as a service to
bioinformatics researchers who don't know the field. When I complete a
draft, I would be tremendously grateful if anyone on this list wanted to
look it over and make sure I am giving an accurate and thorough
portrayal.
>By the way, you may be interested in reading a litle review that I
wrote
>back in 1996. It is centered mostly on the computational techniques
rather
>than the models themselves, but it may still be useful. You can find it
>online at http://gepasi.dbs.aber.ac.uk/pedro/btk96rev.html
I thoroughly enjoyed your review. Actually it was my main jumping off
point for reviewing the literature months ago. Thanks!
