Relay-Version: version B 2.10 5/3/83; site utzoo.UUCP Posting-Version: version B 2.10.1 6/24/83; site sdccs7.UUCP Path: utzoo!watmath!clyde!burl!ulysses!harpo!decvax!ittvax!dcdwest!sdcsvax!sdccs7!ee163ahq From: ee163ahq@sdccs7.UUCP Newsgroups: net.bio Subject: BioComputing summary (Digest Style) Message-ID: <1188@sdccs7.UUCP> Date: Sat, 7-Apr-84 18:01:57 EST Article-I.D.: sdccs7.1188 Posted: Sat Apr 7 18:01:57 1984 Date-Received: Mon, 9-Apr-84 05:11:09 EST Organization: UC San Diego Zoo Lines: 195 Subject: Well, here it is at last: BioComputing Summary '84 Apologies: To those to whom I couldn't directly reply Here's a summary of replies to my question of about a month ago: "What's happening out there?" in terms of computer applications in biology (or biological applications in computing). I mentioned specifically the possibility of determining the quaternary structure of proteins via solutions of Schroedinger's wave equations. R. Martin Chavez of Harvard is planning to take on that problem via extrapolative methods layed down in the AI domain. As for the rest of you, here's what you're doing: [BTW, Usenet sites running readnews should use the d(igestify) command to read this article] From: sdcsvax!decvax!mcnc!jwb (Tue Mar 6 20:34:09 1984) Subject: Re: What's happening out there? We are running simulations of electrical impulse propagation in the heart. These studies combine ionic currents obtained experimentally with models for geometry. The reason for doing this is that the ionic currents can only be obtained under conditions where there can be no propagation (voltage clamp). Understanding electrical propagation is important for the understanding of arrhythmias and how antiarrhythmic drugs work. Jack Buchanan Medicine and Biomedical Engineering University of North Carolina at Chapel Hill decvax!mcnc!jwb From: Hao-Nhien Qui Vu Subject: Re: What's happening out there? Well, I use computer mostly to analyse X-ray photos of virus crystals. The computing load is sky-high, and the resulting model of the crystal is beautiful. ======= Hao-Nhien Vu {eagle, decvax, hao, harpo, ihnp4, seismo, sri-unix, ucbvax, uwvax}!pur-ee!vu or {.......SAME..AS..ABOVE........}!pur-ee!Pucc-K:lcu From: hes@ecsvax.UUCP Subject: DNA Sequence Analysis Date: Tue, 6-Mar-84 13:58:33 PST <> It was mentioned that one of the big new application areas of computation in biology is the storage and processing of DNA sequence data. (Really nucleic acid sequences, but the data is almost all on DNA rather than RNA.) A recent book which covers much of this field (and which has broader coverage than the title suggests) is: Statistical Analysis of DNA Sequence Data edited by B. S. Weir, 1983 published by Marcel Dekker, Inc., NY The chapters are written by different authors and are: 1. Determination of DNA Fragment Size from Gel Electrophoresis Mobility 2. Computers and DNA Sequences: A Natural Combination 3. The Role of Models in the Analysis of Molecular Genetic Data, with Particular Reference to Restriction Fragment Data 4. Statistical Analysis of Restriction Enzyme Map Data and Nucleotide Sequence Data 5. Analysis of Variation in Related DNA Sequences 6. Inferring Evolutionary Trees from DNA Sequences 7. Convergent Evolution and Nonparametric Inferences from Restriction Data and DNA Sequences 8. The Number of Polymorphic DNA Clones Required to Map the Human Genome 9. Use of Restriction Fragment Polymorphisms as Genetic Markers I wrote the first chapter, and will discuss this topic in this newsgroup in the near future. --henry schaffer ncsu genetics From: kovish@mprvaxa.UUCP Subject: Digital analysis of microscopic images Date: Mon, 5-Mar-84 16:16:58 PST Organization: Microtel Pacific Research, Burnaby BC Heres a "BioComputing" idea I have wondered about for a while. Suppose we take a film of some cellular behavior under an optical microscope. This film would then be digitized and processed by a computer. A fourier transform of each image location intensity (color?) as a function of time would be performed. The computer could then insert artificial colors into the image depending upon the time dependent fluctuations in intensity at each image location. More complicated functions of the intensity fluctuations might be developed to color the image. Would the resulting image reveal aspects of cellular behavior not observable normally? Some reasons why it might are: small or quick intensity fluctuations will probably be integrated by the eye and hence invisible; objects too small to be resolved by the optical microscope may still manifest themselves optically by producing intensity fluctuations (only marginally similar to light scattering studies of macromolecules). Has any one tried this? I'm curious what the results were/would be. Thanks for any info. Date: 13 Mar 1984 01:03:04-??? (Tue) From: menlo70!analog!lpi3230!steve We at Linus Pauling Institute are doing some computer work in biology (including DNA and amino-acid sequence analysis, automated analysis of 2D gel electrophoresis data, etc.) but the following Usenet piece sounds more like what you are interested in, so I'm forwarding it to you. If you get any other interesting responses, please forward them (or a summary of them) to me. lpi3230!steve Steve Burbeck Path: lpi3230!analog!menlo70!hplabs!sri-unix!KEDAR-CABELLI@RUTGERS.ARPA From: KEDAR-CABELLI@RUTGERS.ARPA (FORWARDED) Newsgroups: net.ai Subject: III Seminar on Expert Systems this coming Tuesday... Message-ID: <16606@sri-arpa.UUCP> Date: Wed, 8-Feb-84 12:59:49 PST Date-Received: Mon, 13-Feb-84 04:56:57 PST Lines: 61 >From: Smadar [Reprinted from the Rutgers bboard.] I I I SEMINAR Title: Automation of Modeling, Simulation and Experimental Design - An Expert System in Enzyme Kinetics Speaker: Von-Wun Soo Date: Tuesday, February 14,1983, 1:30-2:30 PM Location: Hill Center, Seventh floor lounge Von-Wun Soo, a Ph.D. student in our department, will give an informal talk on the thesis research he is proposing. This is his abstract: We are proposing to develop a general knowledge engineering tool to aid biomedical researchers in developing biological models and running simulation experiments. Without such powerful tools, these tasks can be tedious and costly. Our aim is to integrate these techniques used in modeling, simulation, optimization, and experimental design by using an expert system approach. In addition we propose to carry out experiments on the processes of theory formation used by the scientists. Enzyme kinetics is the domain where we are concentrating our efforts. However, our research goal is not restricted to this particular domain. We will attempt to demonstrate with this special case, how several new ideas in expert problem solving including automation of theory formation, scientific discovery, experimental design, and knowledge acquisition can be further developed. Four modules have been designed in parallel: PROKINAL, EPX, CED, DISC. PROKINAL is a model generator which simulates the qualitative reasoning of the kineticists who conceptualize and postulate a reaction mechanism for a set of experimental data. By using a general procedure known as the King-Altman procedure to convert a mechanism topology into a rate law function, and symbolic manipulation techniques to factor rate constant terms to kinetic constant term, PROKINAL yields a corresponding FORTRAN function which computes the reaction rate. EPX is a model simulation aid which is designed by combining EXPERT and PENNZYME. It is supposed to guide the novice user in using simulation tools and interpreting the results. It will take the data and the candidate model that has been generated from PROKINAL and estimate the parameters by a nonlinear least square fit. CED is a experimental design consultant which uses EXPERT to guide the computation of experimental conditions. Knowledge of optimal design from the statistical analysis has been taken into consideration by EXPERT in order to give advice on the appropriate measurements and reduce the cost of experimentation. DISC is a discovery module which is now at the stage of theoretical development. We wish to explore and simulate the behavior of scientific discovery in enzyme kinetics research and use the results in automating theory formation tasks. -- [That's all folks] -- ThankSalot Doug Salot ..sdcsvax!sdccs7!ee163ahq