Hi folks,
I am a grad student at Stanford in Biomedical Informatics, working in Peter
Karp's lab at SRI. I am currently writing a review on modeling methods in
metabolism, including kinetic simulations, MCA, etc. I have just come
across this newsgroup and have been fascinated by following the
discussions, and reading the colorful opinions of people whose work I have
been pouring over in the last few months. I'd like to humbly submit a few
questions that I would *love* to hear the subscribers of this group to
weigh in on.
Before I ask my questions, I want to quickly mention the motivation for
this paper. Peter and I began an exploration this summer into the idea of
storing kinetic information in Ecocyc so that people could automatically
generate kinetic models from the knowledge-base. Our underlying mistaken
assumption, though it took us a few months to figure it out, was that
kinetics was like genomics -- one community of people was busy spewing out
volumes of reliable data for public consumption, while another set of
people was trying to intergrate all this information from big databases to
build models. One of the main goals of writing this paper from my point of
view, besides describing the state of the art, is to educate the
bioinformatics community about how the field of kinetic modeling really works
So on to my questions. I would be thrilled to hear opinions on any or all
of these. Of course, I don't want to tunnel people's responses through my
own peculiar articulations of the questions, so if anyone has any advice
they want to offer about a really important paper, or contribution of
metabolic modeling, or issue in the field that should be communicated to
the world of bioinformatics, please, spout away...
1. There have been many approaches to metabolic modeling. Kinetic
simulation and MCA seam to be the most widely used, but I have also seen
papers on the use of , e.g. Discrete event based models, Petrinets,
Tendency Modeling, etc. What do you see particularly promising (or not
promising) techniques for generating what types of insights about metabolism.
2. What are the prospects for larger-scale modeling projects like the
NIGMS's projected 25$ glue grant for a "Virtual Cell." Is this a naive and
premature waste of money, or will it be a fountain of knowledge.
3. What is the relation between metabolic modeling and informatics? What
if anything can the field of metabolic modeling gain from the genomics
explosion?
4. What is really the role of all of the metabolic simulation software
packages I see out there, such as Gepasi, SCAMP, Mist, DBSolve, Kinsim,
SCOP, etc. Are these widely used? What factors have led to their adoption?
Thanks so much to anyone who replies to this posting. I have really
enjoying reading the work of many of the subscribers of this list.
Cheers,
Mike Cantor
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