ee163ahq@sdccs7.UUCP (04/08/84)
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 <sdcsvax!decvax!pur-ee!Pucc-K:lcu>
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 <KEDAR-CABELLI@RUTGERS.ARPA>
[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