HDTenEightyP/NetNews huggingface dataset:
From: 22742CRB@MSU.EDU ("Robin.Buell")
Newsgroups: bionet.genome.arabidopsis
Subject: Markers and YACs for chromosome 2
Date: 11 Dec 92 20:15:00 GMT
Distribution: bionet

Dear Network,


We are looking for additional RFLP markers on chromosome 2 near the
RFLP marker m251. Does anyone have additional markers in this region
not listed on the Goodman or Meyerowitz maps? Also, has anyone identified
any YACs for marker m251? I would appreciate any available information.
Robin Buell. Michigan State University.
From: bafp3@central.sussex.ac.uk (Neil Butt)
Newsgroups: bionet.genome.arabidopsis
Subject: OSU meeting
Date: 17 Dec 92 12:12:29 GMT
Distribution: bionet
Original-To: arab-gen@uk.ac.daresbury
X-Mailer: ELM [version 2.3 PL11]

I recently read an E-mail enquiring about the Arabidopsis meeting 
at OSU. I also would be interested in any information, or persons 
I could contact in regard to this. I am especially interested in 
the possible costs.

Hope someone can help

Neil Butt
From: ludwig@biology.ucsc.edu (Bob Ludwig)
Newsgroups: bionet.genome.arabidopsis
Subject: Arabs mutant seed request
Date: 17 Dec 92 22:36:32 GMT
Distribution: bionet


We are searching for Arabidopsis Columbia mutagenized (EMS, DEB, etc) M1 or M2
seed that has been outgrown in high (1%-2%) carbon dioxide.

Any leads and/or info would be greatly appreciated. Thanks.

Bob Ludwig
Sinsheimer Laboratories
University of California
Santa Cruz, CA. 95064
USA

e-mail: ludwig@biology.ucsc.edu
From: OT8Y@CORNELLA.CIT.CORNELL.EDU (Leon Kochian)
Newsgroups: bionet.genome.arabidopsis
Subject: (none)
Date: 18 Dec 92 23:47:11 GMT
Distribution: bionet

We are trying to locate an Arabidopsis root cDNA library. Does anyone have any
information on this?

Leon Kochian
US Plant, Soil & Nutrition Lab
Cornell University
OT8Y@cornella.cit.cornell.edu
From: miao@OCELOT.RUTGERS.EDU ("Miao, Zhonghe")
Newsgroups: bionet.genome.arabidopsis
Subject: Arabidopsis ecotypes
Date: 16 Dec 92 21:33:17 GMT
Distribution: bionet

Arabidopsis networker:
    There are a number of arabidopsis ecotypes, such as Landsberg erecta, C24,
columbia et.al..  I wonder if there is a review article or any reference
describing the origin of and genetic relationship among various arabidopsis
ecotypes.  I am paricularly interested in knowing the genetic relationship
between C24 and columbia ecotypes. Isn't that true that C24  is a derivative of
Columbia? I would appriciate it very much if anybody responds to my questions.
From: gvachon@BCM.TMC.EDU (Gilles Vachon)
Newsgroups: bionet.genome.arabidopsis
Subject: new member
Date: 18 Dec 92 17:37:40 GMT
Distribution: bionet

could you please put me on the list?
Gilles Vachon
Baylor College of Medicine
One baylor plaza, room T634
Houston, TX, 77054

Tel (713) 7985095
fax (713) 7976718
e-mail gvachon@bcm.tmc.edu

Thanks.

Newsgroups: bionet.genome.arabidopsis
From: xie@OCELOT.RUTGERS.EDU ("Xie, Shaoping")
Newsgroups: bionet.genome.arabidopsis
Subject: AUG initiation codon consensus sequences
Date: 11 Dec 92 18:22:46 GMT
Distribution: bionet

Dear Arabidopsis Network:

    There are AUG initiation condon consensus sequences in animals and in
plants. Does anyone have such data just in arabidopsis? I would be grateful to
you if any of you could give me the information.

Thanks a lot!

xie@mbcl.rutgers.edu
From: BTNYDWM@MVS.UCC.OKSTATE.EDU
Newsgroups: bionet.genome.arabidopsis
Subject: Andreas Muller (1935-1992)
Date: 16 Dec 92 23:12:00 GMT
Distribution: bionet

To the Arabidopsis Community:

Today I received the following "In memoriam" for
Dr. Andreas Muller from the acting director of the
Institute of Plant Genetics and Crop Plant Research
at Gatersleben:

"It is with regret that we announce the sudden death of our
longstanding colleague.  Through his achievements, over three
decades in Gatersleben, he greatly enhanced the international
reptutation of the Institute.  His pioneering work with the
crucifer Arabidopsis and the genetics of somatic plant cells
has made a significant contribution to the field of plant
genetics.  We will miss Andreas Muller deeply as a friend,
colleague and scientist."

I too will miss one of the important pioneers in Arabidopsis
research.

David Meinke
From: charvey@teal.csn.org (Chip Harvey)
Newsgroups: bionet.biology.computational
Subject: "Prestige" of Journals for Stat Papers
Date: 18 Dec 92 03:16:46 GMT
Distribution: bionet
Organization: Colorado SuperNet, Inc.
Originator: biocomp@lerkim.umiacs.umd.edu


I am seeking help in evaluating the "prestige" of statistical journals and
other journals publishing papers in statistics and ecological and
environmental statistics.

I am supposed to submit a ranking to a federal government panel of non-
statisticians for purposes of valuation of work published by government
researchers.  As is any such ranking, this too is a linear representation of
a multidimensional set of opinions and as such, is controversial.  The
criteria themselves are controversial.  Anyway, among statistical journals,
I anticipate differences based on theoretical/applied slants of the raters. 

The criteria which are to be used in evaluating "prestige" are: 1) degree of
difficulty in getting a paper accepted, 2) level of referee review, 3)
geographic extent of readership, 4) an assessment of the level of scientific
influence of the journal in the specific field (statistics, ecology,
environmental sciences), and 5) the extent to which senior scientists publish
their best papers in the journal.  There are four categories of "prestige"
ranging from "HIGHLY" to "LEAST."  The list of publications is open-ended.

Additionally, the panel is seeking ideas on how to rate the prestige of books,
book chapters, proceedings, etc.

I would appreciate any participation.  Please e-mail your lists, ratings, and
ideas to me, charvey@csn.org.  If there is general interest, I will post the
results.  I am cross-posting this request in bit.listserv.stat-l and
sci.math.stat.


Chip Harvey                                                 charvey@csn.org
National Park Service                                        (303) 969-2807
Air Quality Division 					FAX: (303) 969-2822
From: dld@bruce.cs.monash.edu.au (David L Dowe)
Newsgroups: bionet.biology.computational
Subject: Monash U SEMINAR: A decision graph explan'n of protein 2'ry structure
Date: 9 Dec 92 05:25:09 GMT
Distribution: bionet
Organization: Computer Science, Monash University, Australia
Originator: biocomp@lerkim.umiacs.umd.edu

Hello.   Below are the details of a SEMINAR to be given at Monash University,
Melbourne, Australia on Wednesday 16th December.  (Sorry if I've got too many
countries or too many newsgroups.  Please pardon.)  The approach to protein
(secondary) structure prediction is information-theoretic, and involves
machine-learning techniques.   Further details follow.  Thank you.

_________________________________________________________________
Date: Tue, 8 Dec 92 16:42:30 +110
From: karen@bruce.cs.monash.EDU.AU (karen patricia fenwick
Subject: Seminar 16th December >Status: R

            DEPARTMENT OF COMPUTER SCIENCE MONASH UNIVERSITY CLAYTON
                                     SEMINAR
Time:   Wednesday, 16th December, 1992  at 2.15 pm
Place:  Room 135, Computer Science Building

Topic:  A Decision Graph Explanation of Protein Secondary Structure 
        Prediction

Speaker:Dr. David L. Dowe 
        Department of Computer Science,
        Monash University, Clayton, 3168, AUSTRALIA.

Abstract:

Oliver and Wallace recently introduced the machine-learning technique
of decision graphs, a generalisation of decision trees.  Here it is
applied to the prediction of protein secondary structure to infer a
theory for this problem.  The resulting decision graph provides both a
prediction method and, perhaps more interestingly, an explanation for
the problem.  Many decision graphs are possible for the problem;
a particular graph is just one theory or hypothesis of secondary
structure formation.  Minimum message length encoding is used to judge
the quality of different theories.
It is a general technique of inductive inference
and is resistant to learning the noise in the training data.

The method was applied to 75 sequences from non-homologous proteins
comprising 13K amino acids.
The predictive accuracy for 3 states (Extended, Helix, Other) is in the
range achieved by current methods.  Many believe this is close to the
limit for methods based on only local information.  However, a
decision graph is an explanation of a phenomenon.  This contrasts with
some other predictive techniques which are more "opaque".  The reason
for a prediction can be of more value than the prediction itself.
    _________________________________________________________________
For further details, please e-mail (in the first instance)
karen@bruce.cs.monash.edu.au (on behalf of the seminar co-ordinator) or
(the speaker) dld@bruce.cs.monash.edu.au .

Thank you.
From: ingber@alumni.cco.caltech.edu (Lester Ingber)
Newsgroups: bionet.biology.computational
Subject: Re: Very Fast Simulated Reannealing (VFSR) via Ftp or Email
Date: 9 Dec 92 10:25:31 GMT
Distribution: bionet
Originator: biocomp@lerkim.umiacs.umd.edu


        Very Fast Simulated Reannealing (VFSR) via Ftp or Email
 
My previous announcement did not specify the use of ftp, and
many people unfamiliar with the use of NETLIB and STATLIB were
understandably confused.  This announcement is to remedy that problem.
 
                STATLIB: vfsr v6.30
Interactive:
        ftp lib.stat.cmu.edu
        [login as statlib, your_login_name as password]
        cd general
        get vfsr
Email:
        mail statlib@lib.stat.cmu.edu
        send vfsr from general
 
                NETLIB: vfsr v6.25
Interactive:
        ftp research.att.com
        [login as netlib, your_login_name as password]
        cd opt
        binary
        get vfsr.Z
Email:
        mail netlib@research.att.com
        send vfsr from opt
 
                PATCH: vfsr-diff-6.25-6.30.Z.uu
If you already have vfsr v6.25 from NETLIB, this can be updated using
a patch I'd be glad to send on request.
        strip out text between CUT HERE lines, save to savefile
        uudecode savefile
        uncompress vfsr-diff-6.25-6.30.Z
        mv vfsr-diff-6.25-6.30 VFSR ; cd VFSR
        patch -p1 < vfsr-diff-6.25-6.30
 
v6.30 fixes a bug encountered for negative cost functions, and adds
some printout to make your bug reports and comments easier to decifer.
 
Lester

  ||  Prof. Lester Ingber               ingber@alumni.caltech.edu  ||
  ||  P.O. Box 857                                                 ||
  ||  McLean, VA 22101       703-848-1859 = [10ATT]0-700-L-INGBER  ||
From: ehling@rice-chex.ai.mit.edu (Teresa A. Ehling)
Newsgroups: bionet.biology.computational
Subject: New book on Nanotechnology
Date: 18 Dec 92 03:20:20 GMT
Distribution: bionet
Organization: MIT Artificial Intelligence Lab
Originator: biocomp@lerkim.umiacs.umd.edu

Now available from the MIT Press!




NANOTECHNOLOGY
Research and Perspectives

edited by BC Crandall and James Lewis

Advances in physics, molecular biology, and computer science 
are converging on the capacity to control, with  molecular 
precision, the structure and function of matter. These twenty 
original contributions provide the first broad-based 
multidisciplinary definition and examination of the 
revolutionary new discipline of molecular engineering, or 
nanotechnology. They address both the promise as well as the 
economic, environmental, and cultural challenges of this 
emerging atomic-scale technology.
  Leaders in their field describe current technologies that 
feed into nanotechnology -- atomic imaging and positioning, 
protein engineering, and the de novo design and synthesis of 
self-assembling molecular structures. They present 
development strategies for coordinating recent work in 
chemistry, biotechnology, and scanning-probe microscopy in 
order to successfully design and engineer molecular systems. 
They also explore advances in molecular and quantum 
electronics as well as reversible computational systems and 
the fundamental physical constraints on computation. 
Additional chapters discuss research efforts in Japan and 
present the prospects of nanotechnology as seen from the 
perspective of a microtechnologist.
  The final section looks at the implications of success, 
including the prospects of enormous computational power and 
the radical consequences of molecular mechanical systems in 
the fields of medicine and life extension. 


Contributors: Robert Birge. Federico Capasso. BC Crandall. 
K. Eric Drexler. Gregory Fahy. Richard Feynman. John Foster. 
Tracy Handel. Bill Joy. Arthur Kantrowitz. Joseph Mallon. 
Norman Margolus. Ralph Merkle. Lester Milbrath. Gordon 
Tullock. Hiroyuki Sasabe. Michael Ward.

ISBN 0-262-03195-7   CRANH
381 pp. -- 136 illus., 29 in color 
$39.95, hardcover

[...]
From: jlogsdon@bio.indiana.edu (John Logsdon)
Newsgroups: bionet.biology.computational
Subject: Sequence Data Input Devices: ADVICE PLEASE
Date: 18 Dec 92 03:14:48 GMT
Distribution: bionet
Organization: Department of Biology / Indiana University
Originator: biocomp@lerkim.umiacs.umd.edu


Our lab is doing alot of sequencing and we have decided to look into
"digitizers" for directly inputting the data into computer files.  

We have GCG running on UNIX (SUN) which we access via Macintoshes (we
have no IBM's).  We have been looking into the various integrated
Macintosh program suites (Mac Vector, MacDNAsis, etc.) which seem to
offer their own input devices integrated into their particular program
suite.  Unfortunately, with GCG and support from our local computer guru
(Don Gilbert), we don't see the point of shelling out lots (!!!) of money
for the fancy Mac program suites which we will only use the (front end?)
input software.  

Anyone out there have any recommendations to make?
How about the digitizer that GCG recommends?

Ideally we would be interested in a digitizer with simple Mac software
that would create text files that we could easily move to GCG (and
back?).  

On a slightly different but related note, How about contig assembly
programs (for the Mac)?  This area is the one bit of GCG that we are not
happy with and partially explains why we have been looking into the
above-mentioned suites (but isn't a good enough reason yet to BUY one).
One that we have demo' ed that we like is Sequencher; the problem is that
it uses a hardware lock.  Any other good ones out there? How about the
input devices that go with them?

Thanks in advance for the help.
email replies - I will post a summary.

John
___________________________________________________________
John Logsdon         Department of Biology
                     Indiana University
                     Bloomington, IN  47405
                     (812) 855-2549
                     (812) 855-6705 fax

jlogsdon@bio.indiana.edu
____________________________________________________________
From: SJJ@ICBR.IFAS.UFL.EDU ("JONG, SONG-MUH J")
Newsgroups: bionet.journals.contents
Subject: Conversion of the Journal content received
Date: 14 Dec 92 21:02:00 GMT
Distribution: bionet

Dear netters,

I had trouble to convert the journal content that I received from this newsgroup
into a REFMANAGER-readable format. I have tried BRS-MEDLINE or any other MEDLINE format
with no luck. Can anyone enlighten me the real format that is recognizable
by the REFERENCE MANAGER program?

Thanks!


sjj@icbr.ifas.ufl.edu
From: HXIE@MACC.WISC.EDU (HUIWEN XIE)
Newsgroups: bionet.journals.contents
Subject: off
Date: 12 Dec 92 04:47:00 GMT
Distribution: bionet

Please sign me off. Thanks.
From: jiangky@vuse.vanderbilt.edu (Keyuan Jiang)
Newsgroups: bionet.journals.note
Subject: reviewer selection
Date: 17 Dec 1992 09:48:56 -0600
Organization: UTexas Mail-to-News Gateway
NNTP-Posting-Host: cs.utexas.edu


Has anyone addressed on "how an editor selects a reviewer"? I'd like to
learn something about it.


Keyuan Jiang
Biomedical Engineering & Computing
Vanderbilt University
Nashville, Tn
From: cherry@OPAL.MGH.HARVARD.EDU
Newsgroups: bionet.molbio.bio-matrix
Subject: Re: Beyond GenBank.
Date: 16 Dec 92 15:10:20 GMT
Reply-To: cherry@OPAL.MGH.HARVARD.EDU
Distribution: bionet.molbio.bio-matrix
Organization: Molecular Biology - Mass Gen Hospital

I agree with Brian Foley and Tom Schneider that there is much
information that is being "lost". That is to say because no one is
cataloging all the features of DNA sequences and the interactions of
proteins with DNA sequences that the job is becoming so large that it
will soon be too big a task to undertake. I am also not completely
satisfied with the current state of GenBank's LOCUS and ACCESSION
tags. However I think these two topics are very separate issues. The
first is something that the NCBI cannot do anything about, at the
moment.  The second one they could.

To undertake the cataloging of all the features and promoter
constructs, etc that are being reported in the literature would
require tens of highly trained people. The obvious problem is the
money to hire these people, lots of money.

I don't think it is appropriate to say "NCBI refuses to acknowledge
and deal STRONGLY with this growing disaster". I know this is not the
case. It is a big problem and there must be a demand from the
community that the money be spent. There most be a plan to undertake
this huge task. There are many things that the NCBI is working on and
I do not wish any of these current project to be terminated.

The issue of funding is not trival. Recently I have tried to approach
NSF for funding to do something similar. However I was dealing
specifically with Arabidopsis information. I was flatly told that this
is not something the NSF wishes to fund. They said there had to be a
clear mandate to undertake this kind of project and an understanding
that it would take money from something else. But the NSF seemed to
think this kind of task was better done by a commercial organization.
Now I don't agree was that last point at all but that was their
opinion.

So how about some constructive critizism for what should be done and
much less bashing! Where will the funding come from? How much funding
is required? What other projects will have to be cancelled because of
this new project? How can it even really be accomplished when to do it
correctly you much have a large number of experts that do nothing but
read papers? What changes need to be make in the way information is
reported in the literature? Do you really want all this in a flatfile
database?

Mike Cherry
AAtDB Project
Newsgroups: bionet.molbio.bio-matrix
From: brianf@dna.uvm.edu (Brain Foley)
Subject: Re: Bio Matrix conference.
Organization: Division of EMBA, University of Vermont
Distribution: bionet
Date: Wed, 16 Dec 1992 16:09:20 GMT

At the Biomatrix conference in Waterville Valley New Hampshire a
couple years ago, GenBank was hardly mentioned.  All sorts of other
biological databases were talked about.  One person had a database of
all the legumes in the world (where they grow, what they look like,
what soil type they live in...) another person had a database of video
images of sea life, the types of databases were incredibly diverse.

Why are all these people not using bionet.molbio.bio-matrix to discuss
their latest exciting topics?  Is there a journal of bio-information
that I should be reading instead?  Is CABIOS really all that there is?
A lot of the interesting stuff is really not published in journals.
I'm sure the legume database is more suitably published in a journal
of plant biology than in CABIOS.  After all, the database may just be
an off-the-shelf database software product, it is the data IN the
database that is interesting.  But a breif discussion of such
databases on bionet.molbio.bio-matrix would be quick and painless.  At
least until the traffic on this list grows to the point where it needs
to become moderated and subjected to peer review as journals are now.

It seems to me that 98% of the traffic on the bionet newsgroups comes
from people who are centered around GenBank/EMBL/PIR/SWISSPROT and
such.  How can we get the other computer-savy biologists to start
speaking up?
--
********************************************************************
*  Brian Foley               *     If we knew what we were doing   *
*  Molecular Genetics Dept.  *     it wouldn't be called research  *
*  University of Vermont     *                                     *
********************************************************************
From: darden@UMIACS.UMD.EDU (Lindley Darden)
Newsgroups: bionet.molbio.bio-matrix
Subject: call for posters on computational biology
Date: 19 Dec 92 20:12:13 GMT
Distribution: bionet

Announcement and Call for Poster Abstracts

The Sixth Biennial Meeting of the International Society for the 
History, Philosophy, and Social Studies of Biology will be held at 
Brandeis University near Boston, Massachusetts, July 14-18, 1993.

The IS/HPSSB brings together scholars from diverse disciplines 
including the life sciences, history, philosophy, and social studies of 
science.  The summer meetings are known for innovative, 
transdisciplinary sessions and for fostering informal cooperative 
sessions and discussions.  Areas of interest include genetics, 
molecular biology, immunology, ecology, classification, behavior, 
Darwin and evolution, cognitive and neurosciences, biotechnology, 
biological instrumentation, issues about gender, ethics of science, 
history of biology, biological institutions, biology teaching.

The deadline for submission for oral presentations was December 1 
and sufficient submissions have been received.  The deadline for 
poster presentations is January 31, 1992, and very few have been 
received.

People working on projects in computational biology are especially 
encouraged to submit a one page abstract for a poster.  Submissions 
from students as well as faculty members are encouraged.  This is an 
especially good opportunity for those in the Boston area to introduce 
their computational work to members of this society.

The abstract should include an indication of the posterUs content and 
the kinds of visuals to be used, the poster title, name of presenter(s), 
institutional affiliation, U.S. Mail address, telephone number, and 
email address.     

Two copies of the abstract should be submitted, either by email or 
hardcopy, to Lindley Darden and William Summers by January 31.  A 
third copy (hardcopy only) should be send by U.S. Mail to Patricia 
Williams.  

Cochairs of the Poster Session:
Lindley Darden
Department of Philosophy
University of Maryland
College Park, MD 20742
301-405-5699 (office)
301-474-0037 (home)
email:  darden@umiacs.umd.edu

William Summers
Radiobiology Laboratories
Yale University School of Medicine
333 Cedar Street; P.O. Box 3333
New Haven, Connecticut 06510-8039


IS/HPSSB 93 Program Chair:
Patricia Williams
P.O. Box 69
Covesville, VA 22931
pw9h@poe.acc.Virginia.EDU

Society membership and conference information:
Peggy Stewart
IS/HPSSB Secretariat
Science Studies Center
102 Price House
Virginia Polytechnic University 
Blacksburg, VA 24061
pstewart@vtvm2.cc.vt.edu