HDTenEightyP/NetNews huggingface dataset:
From: lape@cs.utk.edu (Bryon S. Lape)
Newsgroups: tn.talk
Subject: Re: whyforhowcome?
Date: 9 Oct 92 16:35:09 GMT
Organization: University of Tennessee, Knoxville - CS Department
Distribution: world
NNTP-Posting-Host: duncan.cs.utk.edu

In article <ldb96vINN1e0@utkcs2.cs.utk.edu> moore@cs.utk.edu writes:
>
>Most of it coming from preachers.

	I must disagree.  The left seems to be full of it (ok, so they are
not full of hot air, but something else).

>
>Out of the education system?

	No, but I own my own business.  I am getting my degree to keep my
parents happy.  With a degree, one has a 98% chance of being dead or broke
by age 65 if they depend solely on their jobs for income.  This is
according to the Social Security Association.


Bryon


-----------------------------------------------------------------------------
   The American education system only teaches you to go into debt,
		fortunately, I know how to get out.
-----------------------------------------------------------------------------
-- 
-----------------------------------------------------------------------------
   The American education system only teaches you to go into debt,
		fortunately, I know how to get out.
-----------------------------------------------------------------------------
Newsgroups: tn.talk
From: de5@ORNL.GOV (Dave Sill)
Subject: Re: Name that tune, mr. Spock!
Organization: Oak Ridge National Lab, Oak Ridge, TN
Date: Mon, 12 Oct 1992 17:28:14 GMT

In article <ldj2ruINNq9b@utkcs2.cs.utk.edu>, eijkhout@cupid.cs.utk.edu (Victor Eijkhout) writes:
>You provide illumination for the period of time
>delimited by my nativity nd the complete cessation
>of my metabolic functions.

Ugh.  "You light up my life"

>And we will engage in much jubilant activity
>until such time as the male parent chooses
>to reposses the  vehicle of motorized transport.

"We'll have fun, fun, fun, 'til our daddy takes our T-bird away"?

-- 
Dave Sill (de5@ornl.gov)           For every Bill Joy there is a Kirk McKusick.
Martin Marietta Energy Systems     For every Bill Gates there is a Richard
Workstation Support                Stallman.                     --Paul Graham
From: lape@cs.utk.edu (Bryon S. Lape)
Newsgroups: tn.talk
Subject: Re: whyforhowcome?
Date: 9 Oct 92 14:33:44 GMT
Organization: University of Tennessee, Knoxville - CS Department
NNTP-Posting-Host: duncan.cs.utk.edu

In article <mac.58@ur.utk.ed> mac@ur.utk.ed (Richard J. McDougald) writes:
>Whyforhowcome there's never any Tennessee Talk in tn.talk?
 ^^^^^^^^^^^^^

	I believe it is "Whyforknowhow"

	There is talk in Tennessee, but it is all just hot air.


Bryon
-- 
-----------------------------------------------------------------------------
   The American education system only teaches you to go into debt,
		fortunately, I know how to get out.
-----------------------------------------------------------------------------
Newsgroups: tn.talk
From: mac@ur.utk.ed (Richard J. McDougald)
Subject: whyforhowcome?
Organization: University of Tennessee 
Date: Thu, 8 Oct 1992 19:07:55 GMT

Whyforhowcome there's never any Tennessee Talk in tn.talk?
From: MCCAINKW@DUVM.OCS.DREXEL.EDU (Kate McCain)
Newsgroups: bionet.software
Subject: genetic algorithms EDG
Date: 14 Oct 92 12:17:59 GMT
Distribution: bionet

Can anyone recomment a good list for someone fairly involved in genetic
algorithms -- primarily in modelling applications rather than theory of
computation but a general list will do nicely.  The only provision is
BITNET or Internet access -- we don't have Usenet newsgroup access here.

Thanks in advance.

Kate McCain                          "bibliometrics r us"
mccainkw@duvm.ocs.drexel.edu
Newsgroups: bionet.software
From: BIONET@FRCGM51.EARN
Subject: Readseq
X-Envelope-To: bio-software@daresbury.ac.uk
Original-To: bio-software@UK.AC.DARESBURY
Distribution: bionet
Date: Fri, 9 Oct 1992 09:57:00 GMT
X-Vms-To: IN%"bio-software@daresbury.ac.uk"

 
        Hello,
 
        Some time ago, I downloaded the well known program READSEQ from D.
Gilbert onto our Vax/VMS, compiled, linked and run it without any problem.
 
        Now I'd like to have it on our PC's. Problem: impossible to compile
it without severe errors or, in those rare cases where we could link, run
it without run-time errors (stack overflow). I used the Microsoft QuickC
compiler (various releases, including the Windows version).
 
        D. Gilbert mailed me that he is not aware of such problems. Is
there anybody on the net who experienced similar problems? If so, what is
the trick to compile Readseq on a PC?
 
        Thanks for the help,
 
   ---------------------------------------------------------------
  | Jean-Loup Risler                    |                         |
  | CNRS                                |                         |
  | Centre de Genetique Moleculaire     |  Risler@frcgm51.bitnet  |
  | 91190 Gif sur Yvette   France       |                         |
   ---------------------------------------------------------------
From: dbd@THEORY.BCHS.UH.EDU (Dan Davison)
Newsgroups: bionet.software
Subject: GRAIL/NCBI Shells on UH Gene-Server
Date: 16 Oct 92 20:33:33 GMT
Distribution: bionet

The GRAILSHELLS.SHARE and NCBISHELLS.SHARE files posted by
Fotis Macrides today to software-sources are available for e-mail
retrieval and anonymous FTP from the UH Gene-Server.

For e-mail retrieval:
	send vms grailshells.share ncbishells.share
to
	gene-server@bchs.uh.edu
or for those on BITNET
	gene-server%bchs.uh.edu@CUNYVM

For anonymous FTP:
	129.7.2.43, ftp.bchs.uh.edu, in pub/gene-server/vms
        as ncbishells.share and grailshells.share

I don't offhand know what VMS_SHARE format is, but that's what format
these files are in.

Thanks to Fotis for posting these programs. They've been forwarded to
the other molbio archive sites.

dan
gene-server manager
From: gsbs1022@UTSPH.SPH.UTH.TMC.EDU (Zharkikh Andrey)
Newsgroups: bionet.software
Subject: Re: What Genomes have been Sequenced?
Date: 12 Oct 92 13:13:13 GMT
Reply-To: gsbs1022@UTSPH.SPH.UTH.TMC.EDU
Distribution: bionet

Note added in proof:

Jean-Loup Risler at BIONET@FRCGM51.EARN wrote:

>3) About a former posting: in yeast chromosome III, there are 182
>   open reading frames longer than 300 bp (thus coding for proteins longer
>   than 100 aa). Some of them correspond to already known genes, and 145
>   ORFs are novel (see the Nature paper). Note that these figures are
>   consistent with a study of the chrIII transcripts, hence most of these
>   ORFs are actually translated.
...
>That more than 50% of the ORFs in ChrIII do not resemble anything
>previously known is one great information afforded by its sequencing.

As Monte Carlo simulation shows, about 24 of these ORF are expected
to be found by chance (in a random sequence of length 300,000 with
the same base frequencies as in yeast III chromosome: A=0.31, T=0.30,
G=0.19, and C=0.20).

Andrey.
From: francis@monod.Biol.McGill.CA (Francis Ouellette)
Newsgroups: bionet.software
Subject: Re: Info Needed on EMBL-connection status ...
Date: 9 Oct 92 20:16:48 GMT
Distribution: bionet
Organization: McGill University

HYUNERHO@KRSNUCC1.BITNET writes:

>I am wondering about EMBL-Netserv connection status via e-mail
>recent days . Is anybody out there who knows and are willing to
>let me know the connection status or opration status of EMBL ?
>One of my colleague is trying to register his sequence to EMBL
>data library . And any comments would be very helpful to us .
>Thanks for reading me and in advance .

>Sincerely Rhee Hwan-Seok
>Dept. Mol.Biol
>Seoul National Univ.
>e-mail : hyunerho@krsnucc1.BITNET

Well someone at EMBL was telling me (unnamed for the protection of the
innocent) that some over-zealous person had requested 8000 (yes, 8
thousands) seperate files from the email server, and when these were not
comming in (???) had put in the request a second time! (yes, another 8000
files!)

No wonder email to and from Germany has been a bit slow of late!

It is quite an irresponsible thing to do, and the people who did this
should be "reprimended" (like being told that what they did was *very* bad
...  I do not want to suggest that "big brother" should cut anybody off
the net ) and hopefully we can all learn from this and try to make sure it
does not happen again.  

kindest regards to all,

francis



--
| B.F. Francis Ouellette  
| manager, yeast chromosome I project
| dept of biology, McGill university, Montreal, Qc, Canada
| francis@monod.biol.mcgill.ca
From: kristoff@NET.BIO.NET (David Kristofferson)
Newsgroups: bionet.software
Subject: New version of TurboGopher
Date: 16 Oct 92 18:35:31 GMT
Distribution: bionet

From comp.infosystems.gopher:


Another minor release of TurboGopher (1.0.2) is now available from
the University of Minnesota Gopher server and by anonymous FTP from
boombox.micro.umn.edu.

Outstanding Reported Bugs.
-------------------------
None.

(WAIS-Gateway servers were not sending CRLF at the ends of
lines.  TurboGopher was displaying one long line.  This
will be fixed in the WAIS-gateway server.)
Mac back to ISO characters will be put in soon... not this time around...


B = Bug fix.    C = Cosmetic fix.   Q = Quick feature Hack.

Version 1.0.2 (maintenance release) October 15th 1992.
-----------------------------------------------------------------
B  CSO window checkbox disable bug.  [Joel Cooper]
B  ISO a-acute/a-grave transpose, plus more substitutions [Pierre Cormier]
C  Now not dependent on any custom font.  [Kathryn Ruud]
Q  Left and Right arrow-key Previous/Next window cruising.
Q  More feedback when document is saved to disk.
Q  Now can open TurboGopher by double-clicking Bookmark file (no connect)
Q  Creator of saved TEXT documents now configurable.


  - The Gopher Team
From: gsbs1022@UTSPH.SPH.UTH.TMC.EDU (Zharkikh Andrey)
Newsgroups: bionet.software
Subject: Re: What Genome have been Sequenced?
Date: 13 Oct 92 13:27:01 GMT
Reply-To: gsbs1022@UTSPH
Distribution: bionet


 robison1@husc10.harvard.edu (Keith Robison)


>>As Monte Carlo simulation shows, about 24 of these ORF are expected
>>to be found by chance (in a random sequence of length 300,000 with
>>the same base frequencies as in yeast III chromosome: A=0.31, T=0.30,
>>G=0.19, and C=0.20).
>>Andrey.

>	Curiosity: in the ChrIII paper, the claim was made that
>ORFs of >100 amino acids "have 0.2% probability of occurring by
>chance in S.cerevisiae DNA." Is this consisistent with the above
>estimate?

>Reference ginven (I haven't looked it up yet)
>	Sharp & Crowe.  Yeast (1991) 7:657-678.

>Keith Robison

I didn't read the paper, but the Monte Carlo estimate
can be simply supported by the following consideration:

The average ORF length is 64/3 = 21.3  (for equal base contens)

The expected number of ORFs (of any size including zero length)
is 100,000/21.3 = 4687.5

The probability of ORF of size L is   p(1-p)^L   where p=3/64

The probability of ORF of size L>=100 is (1-p)^100 = 0.008222163

The expected number of long ORFs (L>=100) is 4687.5*0.008222163 = 38.54
Considering the complementary chain doubles this amount, 77.

This is quite close to the Monte Carlo estimation, 24*2 = 48
The difference might be due to unequal usage of bases, boundary effects,
including/excluding stop codon to ORF etc.

So, the probability of finding this long ORFs is not too small
as it could seem at the first glance.

Andrey

Newsgroups: bionet.software
From: danj@merlot.gwu.edu (Dan Jacobson )
Subject: Re: Lander's oligo design prog - where?
Organization: George Washington University, Washington, D.C.
Distribution: bionet
Date: Thu, 15 Oct 1992 15:21:53 GMT

In article <15OCT92.09107572.0064.MUSIC@MUSICA.MCGILL.CA> CX13@MUSICA.MCGILL.CA ("Yannick@CX13") writes:
>Fellow CySpacers, a while ago there was a discussion of primer design
>programs and Eric Lander's OLIGO was widely aclaimed. Can somebody point
>me toward an FTP site for this program?
>
>Thanks,
>
>Yannick Pouliot
>Montreal Neurological Institute



Errr, I could be wrong here but I think that you're thinking of the PRIMER
program out of Lander`s lab.


You can obtain PRIMER by anonymous ftp from genome.wi.edu in the 
distribution/primer.0.4 directory.


Happy hunting,


Dan Jacobson

danj@chablis.gwu.edu
Newsgroups: bionet.software
From: dwright@u.washington.edu (David Wright)
Subject: frame-grabber for mac, Image
Reply-To: dwright@u.washington.edu
Organization: University of Washington
Date: Fri, 16 Oct 1992 22:13:16 GMT

We are looking for a good, high resolution frame  
grabber for the macintosh [ci] (to use with the NIH  
Image program).  We have S-VHS cameras that produce  
pretty good images and want to capture single frames  
without loss of detail.  Ability to also do Quicktime  
stuff a plus, but not essential.  

-- David Wright
U. Washington SM-46
Seattle, WA  98195
dwright@u.washington.edu
From: smith@mcclb0.med.nyu.edu
Newsgroups: bionet.software
Subject: Re: NIH Guide
Date: 8 Oct 92 01:37:29 GMT
Distribution: bionet,world
Organization: NYU Medical Center, New York, NY 10016, USA

In article <9210071519.AA02003@darwin.sfbr.org>, bdyke@DARWIN.SFBR.ORG (Bennett Dyke) writes:
> Does anybody know of a script that will organize, extract, format, etc.
> the electronic version of the NIH Guide?  Thanx in advance...

We have written and made available programs to accept the incomming E-Guide, 
create a database with it and present it to a user.  The user program allows 
searching on text items and NIH keywords, printing, file extraction, mailling 
or whole Guides, or selected fragments of them.  The program also performs 
automatic updating of guide items as errata are posted.

To get a copy, send mail to our MAILSERVer (MAILSERV@MCCLB0.MED.NYU.EDU) with 
the lines HELP and INDEX in the body of the message.  Then follow the 
instructions.  The program is for VAX/VMS and the distribution is packaged 
using VMS_SHARE.

+----------------------------------------------------------------------------+
|Ross Smith,  Research Computing Resource, Department of Cell Biology, NYU-MC|
|E-Mail:  SMITH@NYUMED.BITNET (BITNET),   SMITH@MCCLB0.MED.NYU.EDU (Internet)|
+----------------------------------------------------------------------------+
From: CX13@MUSICA.MCGILL.CA ("Yannick@CX13")
Newsgroups: bionet.software
Subject: Lander's oligo design prog - where?
Date: 15 Oct 92 13:25:58 GMT
Distribution: bionet

Fellow CySpacers, a while ago there was a discussion of primer design
programs and Eric Lander's OLIGO was widely aclaimed. Can somebody point
me toward an FTP site for this program?

Thanks,

Yannick Pouliot
Montreal Neurological Institute
From: HYUNERHO@KRSNUCC1.BITNET
Newsgroups: bionet.software
Subject: Info Needed on EMBL-connection status ...
Date: 9 Oct 92 06:24:02 GMT
Distribution: bionet

Dear Netters ...

I am wondering about EMBL-Netserv connection status via e-mail
recent days . Is anybody out there who knows and are willing to
let me know the connection status or opration status of EMBL ?
One of my colleague is trying to register his sequence to EMBL
data library . And any comments would be very helpful to us .
Thanks for reading me and in advance .

Sincerely Rhee Hwan-Seok
Dept. Mol.Biol
Seoul National Univ.
e-mail : hyunerho@krsnucc1.BITNET
Newsgroups: bionet.software
From: rbm8p@faraday.clas.Virginia.EDU (Rick MacDonald)
Subject: stereo-viewer source?
Organization: University of Virginia
Date: Wed, 7 Oct 1992 19:13:14 GMT

Where can I order inexpensive stereo-viewers in bulk?  I'm looking for
the devices that aid in viewing the stereo images of chain traces and
electron density maps.

Thanks much for any pointers.

Rick MacDonald
rbm8p@virginia.edu
From: gsbs1022@UTSPH.SPH.UTH.TMC.EDU (Zharkikh Andrey)
Newsgroups: bionet.software
Subject: Re: What Genomes have been Sequenced?
Date: 12 Oct 92 17:29:05 GMT
Reply-To: gsbs1022@UTSPH.SPH.UTH.TMC.EDU
Distribution: bionet

One small addition to my previous estimation of the number of
ORF longer than 100 bp expected by chance:

I considered only one DNA strand. Hence, the total number of 
such long ORFs is about 48, that is 26% of all discovered ORFs (182)
or 33% of all novel ORFs.

Andrey
From: mrmike@geta.life.uiuc.edu (Mike McCaughey)
Newsgroups: bionet.software
Subject: Programmer Wanted
Date: 8 Oct 92 16:14:58 GMT
Organization: University of Illinois at Urbana



                 RESEARCH PROGRAMMER

    The Department of Microbiology, University of Illinois at
Urbana-Champaign, seeks a qualified Research Programmer for the
ribosomal database project (RDP), which functions in a world-wide
capacity to facilitate research in some of the more interesting and
important areas of biology; evolution, microbial ecology, nucleic acid
structure, taxonomy, etc.

   Duties will include work on software for the database, automated
mechanisms for exchanging information with other biological databases
and construction of useful and tools for the user community's handling
of the data.  Duties may also include part-time systems administration
of a Unix/MacIntosh network.

   Experience should include familiarity with Unix and MacIntosh
operating systems, C or Fortran, X-windows, and preferably Prolog.
Knowledge of (and interest in) biology is also highly desirable.
A B.S. or M.S. degree is required (preferably in computer science,
engineering, or in combination with biology).

   Position is full time; duration is dependent upon continuation
of funds (from NSF).  Salary is negotiable;
starting date is as soon as possible after closing date.

   Applicants should send a resume, a summary of relevant
experience, and the names and addresses (incl. electronic)
of three references to: Ms. Carolyn Corn, Administrative
Assistant, Department of Microbiology, Univerisy of Illinois,
131 Burrill Hall, 407 S. Goodwin Avenue, Urbana, IL 61801;
Phone: 217-333-1736.

   To receive full consideration, applications should be received
by November 1, 1992. Interviews may be conducted as soon as
applications are received.  However, all applications that are
received by the above date will be given equal consideration.

The University of Illinois is an Equal Opportunity/Affirmative
Action Employer.
From: KBHATNAG@CCMAIL.SUNYSB.EDU
Newsgroups: bionet.software
Subject: Re: stereo-viewer source?
Date: 7 Oct 92 21:17:47 GMT
Distribution: bionet
Organization: State University of New York, Stony Brook

Aldrich markets stereo viewers made by VCH Verlagsgesellschaft mbH. We bought
a couple for around $50 each. Catalog # is Z 15675-2.

For a bulk order, you may want to inquire from VCH directly at:

           VCH Publishers, Suite 909
           220 East 23rd Street, New York, NY 10010-4606

Kavish
From: mrmike@geta.life.uiuc.edu (Mike McCaughey)
Subject: 3D RNA Editor wanted
Organization: University of Illinois at Urbana
Date: Thu, 8 Oct 1992 01:11:41 GMT


Colleagues, 

   I am in search for a computer graphics 3D editing tool to esily
compose RNA and protein spatial structure models at low as well as
atomic resolution. Known structure element coordinates for e.g.
tetraloops, stacks, helices, bends, pseudoknots and for protein
zippers, fingers, sheets, a-helices etc etc should be part of a
toolbox where one can pick structure templates for the buildup.
Structures must be seen and treated with varying detail, for example
an RNA A-helix is either a simple cylinder, a carved cylinder (showing
grooves), same with bases and sugars shown as simple tiles, and with
atoms shown. Only X-ray (and sometimes NMR) data justify the latter,
but lower resolution models from other data can be very useful. I have
seen MacroModel, Insight, Quanta, and brochures for Sybyl/Biopolymer
module. The focus of these programs are either molecular dynamics or
the price is out of line. Would any readers of this know reasonably
priced programs like described, either finished or in the works?

                                          Sincerely, Niels Larsen


           E-mail niels@darwin.life.uiuc.edu   
          _____________________________________________________________________
         /                                                            ______  /
        /  Department of Microbiology    /  1611 B Lyndhurst West    /     / /
       /  University of Illinois        /  Savoy, IL 61874          /_____/ / 
      /  131 Burrill Hall              /  U.S.A.                           /
     /  407 South Goodwin Avenue      /                                   /
    /  Urbana, IL 61801, U.S.A.      /  --------------------------       /
   /                                /  --------------------------       /
  /  Phone  (217)-333-9369         /                                   /
 /  Shared FAX (217)-244-6697     /  (217)-356-5451, ans. mach.       /
/____________________________________________________________________/
From: mplatt@MEDUSA.UNM.EDU
Newsgroups: bionet.software
Subject: (none)
Date: 8 Oct 92 21:19:01 GMT
Distribution: bionet

Does anyone know how to access the "cambridge x-ray crystalography data base?
i.e mail address etc. and any recommendations for mac display programs for
the coordinate data received,
thanks.. Mark Platt Univ. of New Mexico
Mark Platt    ......  ............"it was the best of times
School of Medicine ......   it was the worst of times"
Dept of Microbiology .....
Albuquerque ......  .................
NM 87131

Newsgroups: bionet.software
From: James Petts <pettsj@visigoth.demon.co.uk>
Subject: GDE for SGI machines??
Organization: No Affiliation
Date: Tue, 13 Oct 1992 15:15:19 GMT
X-Useragent: Nuntius v1.1

Can somebody point me in the direction of GDE for the SG please?


James Petts

********************************************************************
* "We use the classical theory on Mondays, Wednesdays and Fridays, *   
*  and the quantum theory on Tuesdays, Thursdays and Saturdays."   *
************************************** Wm. Bragg *******************
Newsgroups: bionet.software
From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert)
Subject: Re: GDE for SGI machines??
Organization: Biology, Indiana University - Bloomington
Date: Tue, 13 Oct 1992 22:23:09 GMT

I picked this out of the bionet news archive using Gopher (to ftp.bio.indiana.edu,
  the item Network-News/Bionet News at IUBio Archive <?>

- - - - - -
From: ajp2o@crocus.medicine.rochester.edu (Anthony J. Persechini)
Newsgroups: bionet.software
Subject: GDE2.0 software package
Keywords: GDE2.0, Irix4.0.x
Date: 25 Aug 92 18:58:59 GMT
Reply-To: ajp2o@crocus.medicine.rochester.edu
Organization: University of Rochester

A port of Steve Smith's GDE (Genetic Data Environment)
package for Silicon Graphics machines running Irix4.0.x is
now available for anonymous ftp on crocus.medicine.rochester.edu 
(128.151.16.31). This port has not been exhaustively tested, but everything
seems to work properly. As noted in the README file,
I am supplying this port as-is, but am willing to address
reproducible port-specific problems (i.e., core dumps) as time permits.

For additional details, see the README file. Binaries only
are available at present.

-- 
Anthony Persechini
Assistant Professor
University of Rochester School of Medicine
ajp2o@crocus.medicine.rochester.edu
Newsgroups: bionet.software

 

-- 
Don Gilbert                                     gilbert@bio.indiana.edu
biocomputing office, biology dept., indiana univ., bloomington, in 47405
Newsgroups: bionet.software
From: hgompf@reed.edu (Heinrich Selwyn Gompf)
Subject: conserved sequences for probe
Organization: Reed College, Portland, OR
Date: Thu, 8 Oct 1992 00:19:02 GMT

Hi, I need to find a highly conserved region of the EGF subfamily of genes
to use as an oligonucleotide probe for a cDNA library.  I know that 
genbank used to do those things, but the Blast and Fetch programs don't seem
to be doing what I want them to.  Could you send me an E-mail with
help? I'm     hgompf@reed.edu
thanx
Newsgroups: bionet.software