Apparently this didn't make it to the newsgroup.....so I'm sending it again
Herbert Sauro
"Mike Cantor" <mcantor at SMI.Stanford.EDU> wrote in message
news:4.2.0.58.20001212135204.01bb9ec0 at smi...
> 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
>>> ---
