Cell Simulation

Herbert M Sauro hsauro at cds.calxxxtech.edu
Tue Oct 24 16:23:10 EST 2000

Sounds an extremely ambitious project. First question is what is the
software product that you're going to convert?
Second question is how will you go about using the static information in
genomic databases to work out an activities path? Assuming that you can do
this, the number of possible paths from your initial to your final
conditions will be huge, how will you know which ones occur in the cell and
which ones are fake? Do you honestly think it is possible to specify a
cancerous cell in detail (if it were possible surely someone would have
developed a cure by now?)? I didn't think they knew that much about the
detailed mechanism of cancer?

Herbert Sauro

"Rich Cooper" <richcooper1 at mindspring.com> wrote in message
news:8skpug$1at$1 at slb6.atl.mindspring.net...
> I'm planning to convert my software product into a cellular activity
> simulation product.  The researcher would specify the initial condition of
> the cell, and specify the final condition, and then the software would use
> genetic function databases to stitch together the sequence of activities
> objects that would drive the cell from the initial condition to the final
> condition.  The researcher would then browse through the stitched together
> activities that a cell might use to perform the sequence of activities.
> For example, you might specify a healthy cell in the details that interest
> you.  Then you might specify a cancerous cell in details using the same
> vocabulary of genes, proteins, activities, and physical objects.
> My background is PhD in CS&EE.  My medical engineering background is
> primarily in physiology, at the organ level, with little chemical
> background.  I've read all the popular genetics books, as well as Watson's
> "Recombinant DNA" classic.  I'm aware of the MitoMap and the Gene Ontology
> Consortium databases.  These might provide a starting vocabulary for cell
> simulation specifications.
> I'm looking for biochemist partners to help define what the product should
> do, and how it should be provided.  If you have any interest in guiding
> directions that a cell simulation product should take, please let me know.
> You can answer the post here, or you can email me directly at:
> mailto:richcooper1 at mindspring.com
> Sincerely,
> Rich Cooper

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