HDTenEightyP/NetNews huggingface dataset:
From: Rob_Last@QMRELAY.MAIL.CORNELL.EDU ("Rob Last")
Newsgroups: bionet.genome.arabidopsis
Subject: Plant Molecular Bio. Fellow
Date: 31 Dec 92 16:35:20 GMT
Distribution: bionet


                       Subject:                               Time:11:28 AM
  OFFICE MEMO          Plant Molecular Bio. Fellowships       Date:12/31/92
Dear Colleagues,
We are soliciting your comments concerning the NSF Postdoctoral Fellowship
Program in Plant Biology.  At a recent meeting on plant biochemistry, several
scientists emphasized the importance of these fellowships for attracting new
researchers into the plant sciences.  We wish to convey to NSF, and the rest of
the scientific community, the impact that this program has had on increasing
the overall quality of plant molecular biology by attracting high quality,
productive scientists from other areas into the field of plant biology.  We
would appreciate receiving your comments on the NSF fellowship program, both
pro and con.  Please send your
comments concerning this program to Rob Last: by Fax: (607) 254-1242; Mail:
Boyce Thompson Institute, Cornell University, Tower Rd.. Ithaca, NY 
14853-1801, or Email: rob_last@qmrelay.mail.cornell.edu, before February 1,
1993. We will then write a consensus letter reflecting the comments that we
receive about the NSF plant postdoctoral program for
submission to one of the American plant molecular biology journals.
Thank you for your input on this important program.  Please distrubute this
posting to any interested colleagues.
Sincerely,
Gloria Coruzzi, New York University
Robert Last, Boyce Thompson Institute
From: savidge@JEEVES.UCSD.EDU
Newsgroups: bionet.genome.arabidopsis
Subject: subscribe to arabidopsis newsgroup
Date: 29 Dec 92 22:51:45 GMT
Distribution: bionet

Please add my name to the arabidopsis newsgroup.

Thanks
From: tmo@POPGEN.BIOLOGY.UMT.EDU (Thomas Mitchell-Olds)
Newsgroups: bionet.genome.arabidopsis
Subject: Finding close flanking markers
Date: 23 Dec 92 18:19:24 GMT
Distribution: bionet

Recently zrsung@insect.berkeley.edu asked:

>Dear members of Arabidopsis community,
>I'm in a desperate need of new (not listed on H. Goodman &
>E.Meyerowitz maps) RFLP markers on chromosome 5.They should be close to
>the RFLP  marker m247. 
>Also, I'm  looking for YAC clones for the marker m247.
>Any information regarding this matter will be appreciated.
> Chang-Hsien Yang, Dept.of Plant Biology, UC Berkeley /

In the absence of mapped markers that are very close to an area of interest, 
a strategy based on bulk segregant analysis may be helpful.   Michelmore 
(PNAS 88:9828) and Skolnik (PNAS 89:1477) have had good success with a similar methods.

1) Obtain the Dupont recombinant inbred lines from the Ohio stock center.

2) Get the RFLP genotypes for these lines from the Arabidopsis database.

3) For markers near your region of interest, identify recombinant inbred
lines fixed for each allele at nearby markers.  Make pooled DNA from individuals
in each group, and compare RAPD markers between the two groups.  Polymorphic markers
in the region of interest will show differences between the two DNA pools,
while markers elsewhere in the genome will give identical banding patterns. 
For example, assume the Arabidopsis genome is 500 cM, and your bulk segregant
analysis compared individuals differing over 10 cM.  On average, 2% of your
RAPD markers will be in the 10 cM region near your gene.  Assuming two
polymorphic bands per RAPD primer, you could screen 500 primers (1,000 loci),
and find about 20 markers near your gene.  On average, several markers should be less
than 0.5 cM from your gene.  You have a 95% chance that your gene of interest is
flanked by two RAPD markers defining an interval SMALLER than 0.75 cM.  These
nearby RAPDs can then be used to identify cosmids or YACs.  This strategy would
be much easier if DuPont would release information on their mapped primers.

Good luck!

Tom Mitchell-Olds
tmo@selway.umt.edu
From: CHERRY@FRODO.MGH.HARVARD.EDU (Mike Cherry 726-5955)
Newsgroups: bionet.genome.arabidopsis
Subject: Arabidopsis Gopher Public Access Account can now sent e-mail
Date: 30 Dec 92 15:47:21 GMT

[Note from D. Kristofferson - There may have been a mail interuption
yesterday.  I am reposting three messages from Mike Cherry.  I'd like
to find out if anyone on the Arabidopsis mailing list received these
previously.  We already know that the USENET distribution worked.
Thanks in advance.]

The public access account to the Arabidopsis Research Companion has
been improved so that you can now e-mail information you have found to
yourself or anyone else. The public access account is available by
using telnet to the hostname ochre.mgh.harvard.edu, the username is
GOPHER and the password is thaliana.

The software provides an option to mail a text file or an entry from
one of the many databases available via gopher/wais. First view the
file of interest or make a query to one of the databases and then view
the information. After viewing the file or database entry the
following prompt will be seen:

        Press <RETURN> to continue, <m> to mail:

Simply press the "m" key then the return key and you will be asked for
an electronic mail address.  Please type carefully. You should enter
your full and complete Internet electronic mailing address.  Note: UK
users must reverse the hostname portion of their Janet address, eg.
Janet: user@uk.ac.cam.vax converted to the Internet format:
user@vax.cam.ac.uk

A Bitnet address can also be used eg. the bitnet address:
343476A@VM45XF would be entered as: 343476A@VM45XF.bitnet

This public access account is provided by the Department of Molecular
Biology at Massachusetts General Hospital in Boston.

Mike Cherry
AAtDB Project
From: CHERRY@FRODO.MGH.HARVARD.EDU (Mike Cherry 726-5955)
Newsgroups: bionet.genome.arabidopsis
Subject: Arabidopsis Gopher Public Access Account can now sent e-mail
Date: 30 Dec 92 15:47:21 GMT
Distribution: bionet

The public access account to the Arabidopsis Research Companion has
been improved so that you can now e-mail information you have found to
yourself or anyone else. The public access account is available by
using telnet to the hostname ochre.mgh.harvard.edu, the username is
GOPHER and the password is thaliana.

The software provides an option to mail a text file or an entry from
one of the many databases available via gopher/wais. First view the
file of interest or make a query to one of the databases and then view
the information. After viewing the file or database entry the
following prompt will be seen:

        Press <RETURN> to continue, <m> to mail:

Simply press the "m" key then the return key and you will be asked for
an electronic mail address.  Please type carefully. You should enter
your full and complete Internet electronic mailing address.  Note: UK
users must reverse the hostname portion of their Janet address, eg.
Janet: user@uk.ac.cam.vax converted to the Internet format:
user@vax.cam.ac.uk

A Bitnet address can also be used eg. the bitnet address:
343476A@VM45XF would be entered as: 343476A@VM45XF.bitnet

This public access account is provided by the Department of Molecular
Biology at Massachusetts General Hospital in Boston.

Mike Cherry
AAtDB Project
From: hantuo@utu.fi (Hanna Tuomisto)
Newsgroups: bionet.biology.tropical
Subject: Re: Is there anyone interested in tropical forest research?
Date: 30 Dec 92 12:09:43 GMT
Organization: University of Turku
X-Useragent: Nuntius v1.1a2

Una,
Thanks for the hint of contacting the local administrator. Didn't know it
works that way.

>>Another nice thing would be some
>>kind of a permanently available list of people who have expressed their
>>interest in this kind of communication, including their e-mail and
postal
>>addresses and perhaps a short note of main interests and research
topics.
>>Any comments on this?
>
>I think the idea is excellent!  Would you care to take charge?

Actually I was hoping that somebody else would take charge. But I guess
everybody else hopes the same so perhaps I could.

>A number
>of people have told me they'd like to get in touch with other tropical
>biologists, and I have forwarded their addresses to other people I know.
>It is not appropriate to put someone on a mailing list (or a list that
could
>be used for unwelcome mailings) without the explicit permission of that 
>person.  So I have not posted my list of fellow tropical biologists:  I
>leave it up to them to do so.

What I suggest is that people who want to be included in the list send to
me their e-mail and postal addresses, together with any additional
information they think the colleagues should know. After some time I'll
e-mail the list to everybody who is included, and send to
bionet.biology.tropical a note to tell what the current situation of the
list is. Thereafter I'd update the list as new addresses come in, and
send the updated list to the participants and an update note to the
newsgroup. But I'm not inclined to do much typing, so I would like to
have all entries sent by e-mail so that they can easily be copied to the
list.
Does anybody have a better idea or do we proceed with this one?

Hanna Tuomisto
hantuo@utu.fi
From: hefa@ERE.UMontreal.CA (He Fangliang)
Newsgroups: bionet.biology.tropical
Subject: Is there anyone interested in tropical forest research?
Date: 23 Dec 92 16:17:51 GMT
Organization: Universite de Montreal

I am working on the tropical forest research in this moment. I
would like to connect to anyone who is interested in that type of
vegetation.

Thanks lot.

Fangliang He
hefa@ere.umontreal.ca
From: GC.GGG@forsythe.stanford.edu (Gwyn Gordon)
Newsgroups: bionet.biology.tropical
Subject: FUNDING ANNOUNCEMENT
Date: 29 Dec 1992 14:45:58 -0800
Organization: Stanford University
NNTP-Posting-Host: morrow.stanford.edu


***FUNDING OPPORTUNITY***

Research Expeditions International is accepting applications for
funding for research projects scheduled for 1994.

Research Expeditions International specializes in Participatory
Research, in which well-educated lay people provide funding and
volunteer as the on-site work force. Studies best suited for
Participatory Research involve data collection or unskilled labor
which is easily taught to one or several groups of adults.
Preference will be given to studies in the following areas: animal
behavior; archaeological excavation; and tourist impact on culture,
economy and ecology. Studies in other fields will certainly be
considered if appropriate.

Applications for the 1994 season are due February 1, 1993.

For informational materials and application, contact:

Gwyn Gordon
gwyn.gordon@forsythe.stanford.edu
415-494-2515
806 Los Robles Avenue
Palo Alto, CA 94306
From: hantuo@utu.fi (Hanna Tuomisto)
Newsgroups: bionet.biology.tropical
Subject: Re: Is there anyone interested in tropical forest research?
Date: 28 Dec 92 13:52:33 GMT
Organization: University of Turku
X-Useragent: Nuntius v1.1a2

Sure, there are plenty of us working in the tropics, but everybody seems
to be hiding in the woods at the moment.
I'm at the University of Turku (Finland) in a group of half a dozen
researchers who spend much of our time walking around to dig ground and
climb trees in Amazonian Peru, trying to find out the geological history
of the area and to establish what kind of vegetation there is in
different places. What is your special interest, He Fangliang?

Una, are you on the line? I'd like to make a few suggestions about this
newsgoup. There have not been very many messages around lately, and
therefore the newsbox has often been empty. But yet the turnover rate
seems to be rather high, and when the messages only stay available for a
short time, they may be missed by many people who only check the
newsgroup occasionally. So I would like to know if it were possible to
leave the messages in for a longer time? Another nice thing would be some
kind of a permanently available list of people who have expressed their
interest in this kind of communication, including their e-mail and postal
addresses and perhaps a short note of main interests and research topics.
Any comments on this?

Some time ago Bill Lawrence wrote that he was interested in contacts with
Amazonian ecologists. I'd be very interested in exchange of ideas, too,
are you still around? 

Hanna Tuomisto
University of Turku, Finland
From: rrk@iris3.chem.fsu.edu (Randal R. Ketchem)
Newsgroups: bionet.biology.computational
Subject: superimpose
Date: 2 Jan 93 18:16:49 GMT
Distribution: bionet
Organization: Florida State University -- Structural Biology Program
Originator: biocomp@lerkim.umiacs.umd.edu


I am looking for a reference that describes the method of superimposing one
molecular structure onto another.

I am trying to superimpose a peptide with one set of torsion angles onto the
same peptide with another set of torsion angles.

Randy

+---------------------------------------------------------------------------+
|Randal R. Ketchem                           ***CELEBRATE FREEDOM***        |
|Institute of Molecular Biophysics            The Holy Bible by God         |
|Florida State University    /_/\/\           1984 by George Orwell         |
|Tallahassee, FL 32306-3015  \_\  /   A Farewell to Arms by Ernest Hemingway|
|904.644.7798                /_/  \  The Catcher in the Rye by J.D. Salinger|
|                            \_\/\ \   Flowers for Algernon by Daniel Keyes |
|Internet: rrk@sb.fsu.edu       \_\/         ***READ A BANNED BOOK***       |
+---------------------------------------------------------------------------+
From: ingber@alumni.cco.caltech.edu (Lester Ingber)
Newsgroups: bionet.biology.computational
Subject: Very Fast Simulated Reannealing (VFSR) v6.35 in Netlib
Date: 18 Dec 92 13:47:07 GMT
Distribution: bionet
Originator: biocomp@lerkim.umiacs.umd.edu


                Very Fast Simulated Reannealing (VFSR) v6.35
 
Netlib requested an early update, and VFSR v6.35 is now in Netlib
and soon will be updated in Statlib.  The code is stable, and is
being used widely.  The changes to date typically correct typos and
account for some problems encountered on particular machines.
 
                NETLIB
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
 
                STATLIB
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
 
		EXCERPT FROM README
2.  Background and Context
 
     VFSR  was  developed  in  1987 to deal with the necessity of
performing adaptive global optimization on multivariate nonlinear
stochastic  systems[2].   VFSR was recoded and applied to several
complex systems, in combat analysis[3],  finance[4],  and  neuro-
science[5].   A  comparison  has  shown  VFSR to be superior to a
standard genetic algorithm simulation on a suite of standard test
problems[6],  and  VFSR  has  been  examined  in the context of a
review of methods of simulated annealing[7].  A project comparing
standard  Boltzmann  annealing  with "fast" Cauchy annealing with
VFSR has concluded that VFSR is a superior algorithm[8].  A paper
has  indicated how this technique can be enhanced by combining it
with some other powerful algorithms[9].


|| Prof. Lester Ingber                         [10ATT]0-700-L-INGBER ||
|| Lester Ingber Research                        Fax: 0-700-4-INGBER ||
|| P.O. Box 857                           Voice Mail: 1-800-VMAIL-LI ||
|| McLean, VA  22101                EMail: ingber@alumni.caltech.edu ||
From: tg@oslovphs.no (Terje Gloersen)
Newsgroups: bionet.biology.computational
Subject: Has anyone heard of the software PC Mensch
Date: 18 Dec 92 11:23:25 GMT
Distribution: bionet
Organization: oslovphs
Originator: biocomp@lerkim.umiacs.umd.edu

I have the German version of the software PC Mensch from M&T Software 
Partner International GmbH.

Does anyone know if there is an English or Norwegian version of this program?
If there is, where can I get a hold of it? And how much does it cost?

Thank you.

Terje Gloersen
tg@oslovphs.no
From: dld@bruce.cs.monash.edu.au (David L Dowe)
Newsgroups: bionet.biology.computational
Subject: Seeking (Mexican) e-mail address of M A Jime'nez-Montan~o
Date: 28 Dec 92 10:24:47 GMT
Distribution: bionet
Organization: Computer Science, Monash University, Australia
Originator: biocomp@lerkim.umiacs.umd.edu


   Hello.   I seek the e-mail address of Dr. M. A. Jimenez-Montano,
(once (1984)) at   Institute of Basic Sciences
                   University of Veracruz
                   91000 Xalapa, Veracruz
                   MEXICO                     ,   and author of

"On the syntactic structure of protein sequences and the concept of grammar
complexity", Bulletin of Mathematical Biology Vol. 46, No. 4, pp641-659 (1984).

   I seek him partly because his work above has similarities with some
information-theoretic done by (some of) my colleagues and me.  If you know him,
please feel invited to pass this message on to him.

Thank you y Gracias.             - David Dowe.

(Dr.) David Dowe, Dept of Computer Science, Monash University, Clayton,
Victoria 3168, Australia           dld@bruce.cs.monash.edu.au
From: ma690188@mbcr.bcm.tmc.edu (R. Mark Adams)
Newsgroups: bionet.biology.computational
Subject: Protein tertiary structure prediction
Date: 27 Dec 92 21:39:17 GMT
Distribution: bionet
Organization: Baylor College of Medicine, Houston, Tx
Originator: biocomp@lerkim.umiacs.umd.edu

Is anyone familiar with the current state of the art in tertiary
protein structure prediction by computer?  It has been a while since
I have looked into this, and I am wondering if there have been any
successes in applying computational methods to 3d protein structure
prediction.  I am aware that many researchers doubt even the
ability of computational methods for predicting secondary structure,
but I am curious if any tools exist for tertiary structure prediction.

Specifically, are programs available for prediction of tertiary
structure for globular proteins from primary protein sequence data?


Thanks!

R. Mark Adams
ma690188@mbir.bcm.tmc.edu

Baylor College of Medicine
Department of Cell Biology
From: aa002@Freenet.carleton.ca (Jay Weston)
Subject: what's this?
Reply-To: aa002@Freenet.carleton.ca (Jay Weston)
Organization: The National Capital Freenet
Date: Mon, 21 Dec 1992 15:21:26 GMT

What is this group all about?  Anyway?
-- 
Jay Weston                              Internet: jweston@carleton.ca
Mass Communication                       Freenet: aa002@freenet.carleton.ca
Carleton University                        phone: (613) 729-4731
Ottawa Canada K1S 5B6                        fax: (613) 788-5604
Newsgroups: bionet.journals.note
From: gwellman@magnus.acs.ohio-state.edu (Gregory S Wellman)
Subject: Re: Author's Rights
Organization: The Ohio State University
Date: Sun, 27 Dec 1992 04:52:58 GMT

I have reviewed and written for a journal which blinds the reviewer from the 
author and their affiliation.  Having been on both sides of the writing "coin" 
this is beneficial.  As objective as I try to be as a reviewer, I sometimes get
biased by the work and "search" it over trying to get a hint of where it is
from.  They aren't always able to completely blind it but go to pretty great
lengths to try to.
From: kristoff@net.bio.net (David Kristofferson)
Newsgroups: bionet.journals.note
Subject: Re: Author's Rights
Date: 22 Dec 92 16:31:03 GMT
Organization: BIOSCI International Newsgroups for Biology

kristoff@net.bio.net (David Kristofferson) writes:

>I found it interesting when looking for academic jobs a long time back
>that faculty I spoke to at some small schools felt that reviewers were
>excessively critical of their work versus papers that originated from
>"name" schools.  Of course, there may be other reasons (as I am sure
>scientists from name schools might quickly reply), but I was wondering
>whether or not any journals ever review papers either completely blind
>(no mention of the authors' identity and affiliation) or partially
>blind (e.g., no mention of the affiliation)?  This might be an
>interesting experiment?!?

I probably shot this one off too quickly as I realized a few seconds
after sending that most authors' propensity to reference their own
past work far more than that of others would make blind reviewing
rather difficult unless one were to gut the paper of such references
which would not be practical in most cases.

				Sincerely,

				Dave Kristofferson
				BIOSCI/bionet Manager

				kristoff@net.bio.net

Newsgroups: bionet.journals.note
From: muriana@aclcb.purdue.edu (Peter M. Muriana)
Subject: Re: Author's Rights
Reply-To: muriana@aclcb.purdue.edu
Organization: Purdue University AIDS Center
Date: Wed, 23 Dec 1992 14:38:02 GMT

In article <Dec.21.15.21.10.1992.3147@net.bio.net>, kristoff@net.bio.net 
(David Kristofferson) writes:

>....... faculty I spoke to at some small schools felt that reviewers were
>excessively critical of their work versus papers that originated from
>"name" schools. 
>........ but I was wondering whether or not any journals ever review papers
> either completely blind (no mention of the authors' identity and affiliation)
> or partially blind (e.g., no mention of the affiliation)?  This might be an
>interesting experiment?!?
>>				Dave Kristofferson

	and, and, and, - how about adding the names of the reviewers **on** 
	the journal article as well (replace a dissenting reviewer by the
	journal editor when a split decision is over-ruled).  
	This would likely insure *better* reviews as well as give credit
	to those who perform such thankless tasks as journal reviews.

Merry Christmas,
Peter M. Muriana
From: agb16@mbuc.bio.cam.ac.uk (Alan Baxter)
Newsgroups: bionet.journals.note
Subject: Re: Author's Rights
Date: 24 Dec 92 07:55:58 GMT
Organization: U. of Cambridge, England

With regards to:

"and, and, and, - how about adding the names of the reviewers **on** 
the journal article as well (replace a dissenting reviewer by the   
journal editor when a split decision is over-ruled).                
This would likely insure *better* reviews as well as give credit"

I have advocated this for quite a while, so long as their names are
shown if accepted outright. What about the reviewers who haggle over
several drafts or ask for huge changes or extensive work - you know,
the ones you would kill if you knew who they were!
Certainly if the editor overrides the reviewers then that should be
stated on the paper. This occurred recently in Science as the reviewers
were outraged that it appeared that they had accepted the paper after
having discussed it extensively with fellow workers (it was a terrible
paper and much of the discussion was about the dubious sanity of the
first author).
Regards Alan
From: kristoff@net.bio.net (David Kristofferson)
Newsgroups: bionet.journals.note
Subject: Re: Anonynimity in the review process (was Authors' rights)
Date: 24 Dec 92 18:35:00 GMT
Distribution: bionet
Organization: BIOSCI International Newsgroups for Biology

Our apologies.  If you receive a bouncer back from this newsgroup with
the note

550 "/usr/local/etc/fm jrnlnote-list"... Can't create output

please ignore it.  Your message was posted.  Kenton is trying to
resolve a bug in the archiving software here which is producing this
problem.  It does not affect distribution of your message, so please
do not repost.

				Sincerely,

				Dave Kristofferson
				BIOSCI/bionet Manager

				kristoff@net.bio.net