From owner-celegans@net.bio.net Tue Dec 10 22:00:00 1996 Path: biosci!cc.umanitoba.ca!gordonr From: gordonr@cc.umanitoba.ca (Richard Gordon) Newsgroups: bionet.celegans Subject: Cyberworm Date: 11 Dec 1996 06:03:38 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 51 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net 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@tripos.com Dick Gordon, University of Manitoba, GordonR@cc.Umanitoba.ca Steve McGrew, New Light Industries, Ltd., stevem@comtch.iea.com Przemko Tylzanowski, University Of Leuven, przemko@sgi.celgen.kuleuven.ac.be Dave Fitch, New York University, fitch@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@cc.UManitoba.ca .