Cyberworm

Richard Gordon gordonr at cc.umanitoba.ca
Wed Dec 11 09:03:38 EST 1996


Nematodes present a unique opportunity for understanding morphogenesis in
what might be called a middle-out manner: from the cells and their
interactions to the organism, and from the cells down to the
mechanochemical physics of the cytoskeleton and the DNA.

We would like to write a 4D database/simulation to be called Cyberworm. As
a database, it would contain and accumulate coordinates, cytoskeletal
arrangements, cell division times, gene expression and other data for each
cell in the developing nematode. Variants, where available, either as
mutants or worms other than C. elegans, would also be included. A rich
color display mode would allow one to visualize this data in 2D, 3D, or 4D
(including time), and label cells by any combination of criteria available
in the database. Cross sections, time lapse sequences, etc., would be
available. Access to the literature and investigators' addresses could be
included. Links to the nematode and other genome databases are possible.

The Cyberworm database/simulation would also be designed to permit modeling
of the mechanisms of morphogenesis and evolution. Thus a finite
element/tensegrity representation of each cell, its division, and its
interactions with neighbors, would be included, along with the ability to
simulate cell-cell diffusion, ionic currents, genetic regulatory networks,
etc., where known. Each parameter would be mutable, and simulation of a
population of Cyberworms "competing" under fitness criteria would be
included. All parameters would be empirical and/or linked by current theory
and compared to empirical values.

Obviously, we will need rich, accurate sources of data for such an
ambitious undertaking. The very exercise of trying to simulate Cyberworm
will uncover areas of ignorance, which different individuals may wish to
tackle.

Your thoughts and offerings for such an undertaking are welcome. We see
this as an open, modular project, where our job will be to design the
skeleton and others who join the project will add their data, hypotheses
and modules in a coherent fashion. The project is not funded, nor
proprietary, and therefore has no constraints.

Randy Zauhar, Tripos, Inc., zauhar at tripos.com
Dick Gordon, University of Manitoba, GordonR at cc.Umanitoba.ca
Steve McGrew, New Light Industries, Ltd., stevem at comtch.iea.com
Przemko Tylzanowski, University Of Leuven, przemko at sgi.celgen.kuleuven.ac.be
Dave Fitch, New York University, fitch at acf2.nyu.edu

--------------------------------------------------------------------
Dr. Richard Gordon, Department of Radiology
University of Manitoba, Room ON104, Health Sciences Centre
820 Sherbrook Street, Winnipeg, MB R3A 1R9 Canada
Phone: (204) 789-3828,  Fax: (204) 787-2080, Home: (204) 589-0411
E-mail: GordonR at cc.UManitoba.ca





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