Cell Simulation

Rich Cooper richcooper1 at mindspring.com
Fri Oct 27 20:11:05 EST 2000

Thanks for your comments, Petr:

> Rich Cooper wrote:
> ...
> > Does anyone see a need for commercially supported simulation
> > services that might provide the support researchers need to conduct
> > very large, very complex simulations?  Something that might be an
> > ASP type of service, with a modest monthly fee ...
> Personally, I think you are probably ahead of your time here.  You are
> asking about the viability of a commercial service in cellular
> simulations, as if there already existed an accepted methodology for
> mathematical simulation of cellular processes.  The fact is, Science
> will have to come before Business here, but in my opinion this kind of
> science is not yet mature enough.
> Please note in the Chemical & Engineering News, October 16, 2000, an
> article on page 24.  You'll see a picture of Nobel laureate Alfred
> Gilman (discoverer of G-protein signaling in cells) sitting in front of
> a computer, talking about the "Alliance for Cellular Signaling"
> (http://afcs.swmed.edu/).  He is the director of this new organization,
> funded by the federal government (National Institute of General Medical
> Sciences) and a dozen pharma companies.
> The idea is to put on the Internet, for a free access by anyone, partial
> results from experimental and theoretical (simulation) studies of
> individual pieces of the cellular signaling puzzle. The "Alliance" folks
> talk about individual "molecule pages", which anyone will be able to
> access and even re-publish in their own papers if they can find use for
> the results.  For speed of publication, there will not be journal
> articles, but the "Alliance" website(s) will be internally
> peer-reviewed.
> ...
> Anyway, it's all just at the beginning.  It'll take quite a few years of
> cranking out tons of experimental data, as well as developing entirely
> new computational strategies, before anyone will be able to build a
> credible mathematical model of a cancerous cell.  I think that is what
> you are interested in selling, but if you look at
> http://afcs.swmed.edu/, you can probably see that the market for your
> service probably isn't there given the state of the basic science in
> this area.

Yes, the AFCS's goals are very much in line with mine.  They want to
build the "Molecule Pages", including tables of data as defined on their
site.  And you're right, the data isn't there yet - they posted a five
year goal and a ten year goal.

My goal is not to get into specific areas of biological research, but to
put together a tool that researchers can eventually use to study disease
processes, in greater detail than they could without the tool.  The tool
should be able to use public databases like the AFCS's, FlyBase,
Mus, and MitoMap.

My goal is to provide a tool that is so useful to researchers that they
are please to pay a reasonable usage fee for the results they get.
Certainly from the start, there will be many databases.  I saw one
web site that claimed there are presently about 500 databases that
make genetic information public.  Surely a tool that could be used
by researchers to unify the vast data resources would be needed.

Is that more in line with the present state of conditions?

Rich Cooper

> Hope this helps,
> - Petr
> P e t r   K u z m i c,  Ph.D.               mailto:pkuzmic at biokin.com
> BioKin Ltd. * Software and Consulting           http://www.biokin.com

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