HDTenEightyP/NetNews huggingface dataset:
From: adm@neuro.duke.edu (Alan Magid)
Newsgroups: bionet.software
Subject: Re: Mac to PC disk utility?
Keywords: file translation
Date: 29 Aug 92 12:38:34 GMT
Distribution: bionet
Organization: Duke University; Durham, N.C.

Another INIT that I favor for the purpose is AccessPC (Insignia,
publishers of SoftPC).
Almost ideal for the purpose though is MacLink/PC. (Dataviz). A cable
between the Mac and PC + a zillion file translators. Very smooth, fast,
and solid. $135 at our college computer shop. MacConnection has it
for mail-order purchase, for example.
Disclaimer: one man's opinion only. I have no connection with any of
the named enterprises. Just trying to help.
-Alan Magid
From: mangalam@SALK-SC2.SDSC.EDU
Newsgroups: bionet.software
Subject: Re: DNA Strider?
Date: 2 Sep 92 23:16:00 GMT
Distribution: bionet

Eric Bowman writes:

>We've been having trouble with DNA Strider 1.1; does anyone know:
>
>o   Does the author have an email address
>o   Is there a new version? (version 1.1 dates from 1989)

   Having just gone thru this, the answers are a) not that anyone has been
able to determine thru netfind, hearsay, bribery, or slander BUT, I do have
an address and fax number:

Dr. Christian Marck
Service de Biochimie et de Genetique Moleculaire
Bat. 142 Centre d'Etudes de Saclay
91191 GIF-SUR-YVETTE      CEDEX        FRANCE
fax: (33 1) 69 08 47 12

 and b) Version 1.2 has been available for a few months, i) for free if you
paid for version 1.1 or ii) for $200 US if you didn't.

   Strider 1.2 retains the familiar interface, speed (!), and simplicity of
the previous versions and adds some useful if primitive primer analysis
tools and diagonal analyses for both DNA and protein.  It allows more
restriction enzymes to be entered into the RELibrary, but it also still
retains the 32.5 Kb limit on sequence 8(.  Is it worth $200?  Unreservedly
YES!

Cheers

Harry


Harry Mangalam                                   Vox:(619) 453-4100, x250
Dept of Biocomputing                                   Fax:(619) 552-1546
The Salk Institute                             mangalam@salk-sc2.sdsc.edu
10010 N Torrey Pines Rd                        mangalam@salk-sgi.sdsc.edu
La Jolla CA 92037                                    mangalam@salk.bitnet
From: danj@WELCHGATE.WELCH.JHU.EDU (Dan Jacobson x-8453)
Newsgroups: bionet.software
Subject: Re:  gene/protein alignments for pub
Date: 31 Aug 92 22:35:27 GMT
Distribution: bionet


Robert Roxby writes:


>If there is a DOS program that makes alignments suitable for
>publication from data files, I would like to know about it.

There is a DOS program which allows you to align sequences
maunually - called esee (EyeBall Sequence Editor) by Eric Cabot.

You can ftp it from ftp.bio.indiana.edu 

in the /molbio/ibmpc directory.

There is also a Windows program for automatic alignment of up to
sequences called MACAW, written by Greg Schuler and friends.

You can ftp it from  ncbi.nlm.nih.gov

in the /pub/macaw directory.


Best of luck,

Dan Jacobson
From: kristoff@GENBANK.BIO.NET (Dave Kristofferson)
Newsgroups: bionet.software
Subject: test, please ignore
Date: 3 Sep 92 17:12:20 GMT
Distribution: bionet


test of bio-soft@genbank.bio.net
From: GOES@edu.umn.cis.vx (Jim Goes)
Newsgroups: bionet.software
Subject: Help, I'm trapped in this newsgroup and can't get out!
Date: 3 Sep 92 21:24:52 GMT
Distribution: bionet
X-Envelope-To: bio-software@daresbury.ac.uk, biosci@daresbury.ac.uk
X-Vms-Cc: IN%"biosci@daresbury.ac.uk",GOES
Original-To: bio-software@uk.ac.daresbury, goes@edu.umn.sph.chimera
Content-Transfer-Encoding: 7BIT
Mime-Version: 1.0
Original-Cc: biosci@uk.ac.daresbury
X-Vms-To: IN%"bio-software@daresbury.ac.uk"

Apologies to the list.  I've tried multiple incantations to signoff
with the daresbury listserver but can't seem to get unhooked. 

Will some kind soul please drop me from this list?  A thousand thanks.
_______________________________________________________________________________ 
Jim Goes                           |BITNET:   GOES@UMNACVX 
Health Management and Policy       |InterNet: GOES@VX.ACS.UMN.EDU
School of Public Health            |Voice:    612/624-3118
University of Minnesota            |Fax:      612/626-3972
From: kupiec@edu.ciwemb.mail1 (Bill Kupiec)
Newsgroups: bionet.software
Subject: re-DNA Strider
Date: 3 Sep 92 08:18:59 GMT
Distribution: bionet
Original-To: bio-software@uk.ac.daresbury


                                                              Time:8:07 AM
Subject:     re:DNA Strider                                   Date:9/3/92
>We've been having trouble with DNA Strider 1.1; does anyone know:
>o   Does the author have an email address
>o   Is there a new version? (version 1.1 dates from 1989)

I'm not sure whether or not he has an E-mail address but his
regular address is:

Dr. Christian Marck
Service de Biochimie et de Genetique Moleculaire
Bat. 142
Centre d'Etudes de Saclay
91191 GIF-SUR-YVETTE CEDEX
FRANCE

The latest version of DNA Strider is 1.2. It was released in August '92 and
includes two more menus and a lot of revisions. Version 1.2 is "32-bit clean"
and runs under both System 6 and 7. It is also compatible with the Quadras and
the PowerBooks.

Hope this helps,
- Bill
*------------------------------------------------------------*
Bill Kupiec
kupiec@mail1.ciwemb.edu, AppleLink: KUPIEC
Computer Systems Manager, Carnegie Institution of Washington
*------------------------------------------------------------*
From: chh9@quads.uchicago.edu (Conrad Halton Halling)
Newsgroups: bionet.software
Subject: Inconsistent use of "/codon_start=" qualifier at EMBL
Date: 2 Sep 92 01:55:28 GMT
Reply-To: chh9@midway.uchicago.edu
Organization: University of Chicago Computing Organizations

I am writing a program that parses the CDS keys of the FEATURE tables
of GenBank and EMBL entries.

I have discovered an inconsistent use of the "/codon_start=" qualifier in
several EMBL entries.

On page 55, "The DDBJ/EMBL/GenBank Feature Table: Definition" manual
(version 1.04) states that the "/codon_start=" qualifier can take values
of 1, 2, or 3 (indicating the relative offset of the reading frame from
the start nucleotide).  However, as in the example below, the qualifier takes
the value of the actual position in the sequence.  (I believe this was the
meaning implied for this qualifier in version 1.03 of the feature table
definition.)  I have not yet observed this problem in GenBank entries.

This sort of thing doubles the work of the programmer, who must test for
both eventualities.

Is this something that will be corrected soon?

Example:
--------

[SSCYS]     Synechococcus sp. cysA, 3' end, spbA, cysT, orf81, cysR, and cysW
     genes, complete cds.

ID [LOC]
     SSCYS      standard; DNA; PRO; 4127 BP.

ACCESSION [ACC]
     M65247;

[ ... several lines omitted ... ]

FEATURES [FEA]
     Key             Location/Qualifiers
     CDS             complement(<1..33)
                     /note="homologous to nucleotide binding
                     polypeptides of other permease systems"
                     /gene="cysA" /codon_start=33
     CDS             233..1285
                     /function="sulfate-binding protein" /gene="sbpA"
                     /codon_start=233
     CDS             1360..2196
                     /note="integral membrane polypeptide of the
                     sulfate permease" /gene="cysT" /codon_start=1360
     CDS             2220..2465
                     /label=orf81                /codon_start=2220
     CDS             2493..3113
                     /gene="cysR"                /codon_start=2493
     CDS             3159..4019
                     /note="integral membrane polypeptide of the
                     sulfate permease" /gene="cysW" /codon_start=3159


-- 
Conrad Halling
c-halling@uchicago.edu
From: bowman@reed.edu (Eric Bowman (bobo))
Newsgroups: bionet.software,comp.sys.mac.apps
Subject: DNA Strider?
Date: 2 Sep 92 21:44:39 GMT
Article-I.D.: reed.1992Sep2.214439.26309
Organization: Reed College, Portland, OR

We've been having trouble with DNA Strider 1.1; does anyone know:

o   Does the author have an email address
o   Is there a new version? (version 1.1 dates from 1989)

On a related note, I was able to hack it so it would run on a SE running
System 7; the unhacked-version gave the informative message that it required
System 6.0.2 to run.  If you want to do this yourself, here's how I did it
(since this is a vaguely commercial program, I can't very well send it, sorry)

In ResEdit, open CODE resource 1 with the hex editor, and replace the words at
offset 1A2 - 1B1 with 8 "4E71"'s.  That is, select the eight words (a word is one
of the 4-number-letter things, and type 4 e 7 1 eight times.  4E71 is the
hexadecimal opcode for "NOP", or no operation.  This just means I removed
the instructions which check to make sure the right system is present.
If you do this, be careful!  Don't run on a system before 6.0.2.

Thanks,
bobo
bowman@reed.edu
George Clinton in '92
From: LEARN@UCRVMS.BITNET
Newsgroups: bionet.software
Subject: PCR primer design software
Date: 1 Sep 92 19:19:00 GMT
Distribution: bionet

I apologize to the network for asking a question that is almost an FAQ:

What methods do you all use to design primers for PCR (primarily) and
sequencing?  We have OLIGO v3.4 in our lab and many of us have tried to use it
with mixed results.  My perception of primer design is that it is a "black box."

1) Has anyone done the experiment comparing the use of OLIGO to a seat-of-the-
   pants, intuitive "method?"

2) Our impression with the results of OLIGO is that it may be too finicky.  We
   use primer-pairs that were designed before we bought software.  We have
   tried to use OLIGO to analyze the primers (which work in at least 75% of a
   broad sample of different angiosperm species) and it predicts that they
   might have problems.  Does anyone have the same experience?

3) Are there reviews in the literature that specifically address the issue of
   designing primers for PCR?  We are familiar with "The Simple Fool's Guide to
   PCR" v2.0 by Steve Palumbi and coworkers.  Is there anything that goes
   beyond this to explain theory of primer design?


Any help that you can provide will be greatly appreciated.  I will summarize
responses.

Thanks,

Jerry Learn
-------------------------------------------------------------------------
| Dept. of Botany & Plant Sciences      |       LEARN@UCRVMS.BITNET     |
| University of California              |       learn@moe.ucr.edu       |
| Riverside, CA  92521                  |       (714) 787-3543          |
| USA                                   |       FAX: (714) 787-4437     |
-------------------------------------------------------------------------
Newsgroups: bionet.software
Subject: Re: Inconsistent use of "/codon_start=" qualifier at EMBL
From: Fuchs@EMBL-Heidelberg.DE (Rainer Fuchs)
Date: 2 Sep 92 07:53:55 +0100
Followup-To: bionet.software
Distribution: world
Organization: EMBL Data Library

In article <1992Sep2.015528.21973@midway.uchicago.edu>,
chh9@quads.uchicago.edu (Conrad Halton Halling) wrote:

> I have discovered an inconsistent use of the "/codon_start=" qualifier in
> several EMBL entries.

> Is this something that will be corrected soon?

This is a known problem which stems from the time when - as you have
guessed - the definition of /codon_start was not exactly clear.
The correction of entries in which this qualifier is used incorrectly is
part of a major clean-up of the feature table which is currently under
progress and should be done before the next release.

Rainer Fuchs
EMBL Data Library
Fuchs@EMBL-Heidelberg.DE
Newsgroups: bionet.software
From: krystek@alcor.bms.com (Stanley Krystek)
Subject: Re: Program to draw polypeptide figures
Organization: Bristol-Myers Squibb, Macromolecular Modeling
Date: Fri, 28 Aug 1992 13:52:29 GMT


I would also like to know if someone has MAC or other system
based programs to draw the polypeptide backbones in the circles.

Thanks in advance...

stan

--
<><><><><><><><><><><><><><><><><><>==*==<><><><><><><><><><><><><><><><><><><>
<>                                                                           <>
<>     .-----.      Stanley R. Krystek, Jr., Ph.D.               .-----.     <>
<>    / \   / \     Bristol-Myers Squibb Pharmaceutical         / \   / \    <>
<>   /   \ /   \    Research Institute                         /   \ /   \   <>
<>   ----- -----    Department of Macromolecular Modeling      ----- -----   <>
<>   \   / \   /    P.O. Box 4000    Room H.3812               \   / \   /   <>
<>    \ /   \ /     Princeton, N.J.  08543-4000                 \ /   \ /    <>
<>     `-----'                                                   `-----'     <>
<>                  (609) 252-4100  FAX: (609) 252-6030                      <>
<>                  INTERNET:  krystek@bms.com                               <>
<>                                                                           <>
<><><><><><><><><><><><><><><><><><>==*==<><><><><><><><><><><><><><><><><><><>
From: kristoff@genbank.bio.net (David Kristofferson)
Newsgroups: bionet.software
Subject: test 3, please ignore
Date: 3 Sep 92 17:13:32 GMT
Distribution: bionet
Organization: GenBank Online Service


test of bionet.software
From: mangalam@SALK-SC2.SDSC.EDU
Newsgroups: bionet.software
Subject: Re: re:- DNA Strider
Date: 3 Sep 92 16:34:59 GMT
Distribution: bionet

>kupiec@edu.ciwemb.mail1 (Bill Kupiec) writes:-
>>The latest version of DNA Strider is 1.2. It was released in August '92 and
>>includes two more menus and a lot of revisions. Version 1.2 is "32-bit clean"
>>and runs under both System 6 and 7. It is also compatible with the Quadras and
>>the PowerBooks.
>>
>>Hope this helps,
>>- Bill
>
Ken Baker:
>Does anybody know of an FTP location for DNA Strider 1.2? I'd very much like 
>to check it out, but when I try the string "strider" on ARCHIE all I get are
>Sisters of Mercy lyrics. 
>Thanks in advance,

   Strider is not free/shareware and thus is not (or should not be)
available at any FTP sites.  That's why all these people want to know how
to get in touch with Christian Marck.

Cheers,

Harry


Harry Mangalam                                   Vox:(619) 453-4100, x250
Dept of Biocomputing                                   Fax:(619) 552-1546
The Salk Institute                             mangalam@salk-sc2.sdsc.edu
10010 N Torrey Pines Rd                        mangalam@salk-sgi.sdsc.edu
La Jolla CA 92037                                    mangalam@salk.bitnet
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Newsgroups: bionet.info-theory
Subject: Re: Limitations of Neural Nets with Quadrature data
Keywords: NN neural nets Eco RI info theory Shannon hyperplane separability
Date: 26 Aug 92 18:09:38 GMT
Organization: Frederick Cancer Research and Development Center

In article <1992Aug26.032203.20189@ncsu.edu> samodena@csemail.cropsci.ncsu.edu
(S. A. Modena) writes:

>Some argued that a neural net ought "to work" by analogy with the
>perceptron "success" for promoter recognition (...feel free to
>correct me).

Before that, ribosome binding sites; after: splice junctions.

>The problem involved with information that is succinctly expressed
>in two bit wide alphabets....the difficulty experienced by perceptrons
>appears to do with the conciseness of expressing four alternative
>states with a two-bit representation.

Actually, the original use of the perceptron did NOT have this problem because
yours truely suggested the alphabetic widening!  The first use of a neural net
to distinguish binding sites from other sequences was Gary Stormo's thesis:

@article{StormoPerceptron1982,
author = "G. D. Stormo
 and T. D. Schneider
 and L. Gold
 and A. Ehrenfeucht",
title = "Use of the {`Perceptron'} algorithm to distinguish translational
initiation sites in {{\em E. coli}}",
year = "1982",
journal = "Nucl. Acids Res.",
volume = "10",
pages = "2997-3011"}

Nobody has gotten around to trying it directly with 4 symbols, as far as I
know.  It just seemed to be not a good idea because it forces a bias into the
results.

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
Newsgroups: bionet.info-theory
From: samodena@csemail.cropsci.ncsu.edu (S. A. Modena)
Subject: Re: bionet.bionette or bionet.women ?
Organization: Crop Science Dept., NCSU, Raleigh, NC 27695-7620
Distribution: bionet
Date: Wed, 2 Sep 1992 22:03:47 GMT

In article <1992Sep2.140415.13115@gserv1.dl.ac.uk> ajt@uk.ac.sari.rri writes:
>In article <9282125555.MIN-LFHCa26691.bionet-news@uk.ac.daresbury> you write:
>: [...]
>: I said, I can stand any name, but I _prefer_ bionette.women.
>                                                     ^^
>Maybe you have hit on the solution to please everyone, Kay: We can just
>rename the entire hierarchy from bionet to bionette ;-)
>
>Seriously though, I agree with Dave's point about the purpose of
>bionet.  I think that a genderless name would have been more
>appropriate in the first place, ...........

Tony, I think you are missing Kay's point:  bionette.women is
the forerunner of a separate, segregant newgroup heirarchy.  The
purpose of bionette is: to discuss obvious and non-obvious obstacles
to women in biology.  

As a UKite, you just are not politically correct enough yet.  ;^)

Steve
---
+------------------------------------------------------------------+
|     In person:  Steve Modena     AB4EL                           |
|     On phone:   (919) 515-5328                                   |
|     At e-mail:  nmodena@unity.ncsu.edu                           | 
|                 samodena@csemail.cropsci.ncsu.edu                |
|                 [ either email address is read each day ]        |
|     By snail:   Crop Sci Dept, Box 7620, NCSU, Raleigh, NC 27695 |
+------------------------------------------------------------------+
         Lighten UP!  It's just a computer doing that to you.
OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
From: hermanh@bio.vu.nl (Herman Hillebrand)
Newsgroups: bionet.general
Subject: Re: what is meant with acera
Date: 26 Aug 92 08:08:26 GMT
Organization: Fac. Biology Vrije Universiteit Amsterdam
X-Useragent: Nuntius v1.1b2

Something went wrong with the editor...

In the title of the film 'Acera ou le bal des sorcieres' by the french
 cineast Jean Painleve, I found the word Acera. I can deduct from 
the description of the film, that it is probably the marine snail
Crepidula fornicata, but this animal is called in french textbooks
'crepidule'. Can anybody suggest the proper latin name?
hermanh@bio.vu.nl
From: samodena@csemail.cropsci.ncsu.edu (S. A. Modena)
Newsgroups: bionet.general
Subject: Re: bionet.bionette or bionet.women ?
Date: 1 Sep 92 06:41:03 GMT
Organization: Crop Science Dept., NCSU, Raleigh, NC 27695-7620

In article <5010@news.duke.edu> una@phy.duke.edu (Una Smith) writes:
>So far, the comments are running 12 to 2 in favor of
>bionet.women rather than bionet.bionette.  The general
>feeling is that '-ette' is distasteful.
>
>	Una
>
>-- 
>
>Una Smith   una@phy.duke.edu    Department of Biology
>                                Yale University
>                                New Haven, CT  06511-7444

With the exception of one open post, Una could be making those numbers up.
Why are there 14 offline expressions of opinions to two online?  

Wasn't the discussion period the time and place to dicuss renaming?
I'd like to hear Cassandra's rationale for her original suggestion of
"bionette." 

Let's name it for what it is: bionet.apartheid......according to
the dictionary:  "apart" = apart   "heid" = -hood....

Steve
---
+------------------------------------------------------------------+
|     In person:  Steve Modena     AB4EL                           |
|     On phone:   (919) 515-5328                                   |
|     At e-mail:  nmodena@unity.ncsu.edu                           | 
|                 samodena@csemail.cropsci.ncsu.edu                |
|                 [ either email address is read each day ]        |
|     By snail:   Crop Sci Dept, Box 7620, NCSU, Raleigh, NC 27695 |
+------------------------------------------------------------------+
         Lighten UP!  It's just a computer doing that to you.
OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
From: collet@scripps.edu (Thomas Collet)
Newsgroups: bionet.general
Subject: Annual Reviews for sale CHEAP!
Date: 30 Aug 92 07:27:21 GMT
Distribution: usa
Organization: The Scripps Research Institute, La Jolla, California, USA

FOR SALE for little more than shipping:

Ann. Rev. Biophys. Biophys. Chem. Vol. 14-17 (1985-1988)

Ann. Rev. Biochem. Vol. 54-57 (1985-1988)

Make an offer. I don't want to have to throw them away.

Thomas            COLLET@SCRIPPS.EDU
Newsgroups: bionet.general
From: nmrdb@vms.macc.wisc.edu (BEVERLY SEAVEY)
Subject: Re: more bionette stuff
Organization:  University of Wisconsin Academic Computing Center
Distribution: bionet
Date:  2 SEP 92 10:02:26    

In article <1992Sep1.161005.1922@gserv1.dl.ac.uk>, amolina@es.cica writes...

> 
>P.S. What would happen if all the men scientists asked to be subscribed
>to bionette?

Probably not very much. I don't imagine that anyone would mind as much as you 
seem to hope.
Newsgroups: bionet.general
From: hiroki@AIX (Hiroki Morizono)
Subject: Re: bionet.bionette or bionet.women ?
Reply-To: hiroki@limerick.cbs.umn.edu
Organization: University of Minnesota
Date: Tue, 1 Sep 1992 05:33:48 GMT

Gee... Should we choose a name that has such a fine, upstanding, descriptive,
feminine diminutive tacked on it like some high school dance line team or
french maid (yes, with all the connotations the term brings) for a group aimed
at furthering a sense of community and equality for women biologists? 
Someone's subconscious was working overtime at sabotage when they came 
up with that name... Who's gonna take credit for it? Anyone?  :-)

Can you "legally" change the name of a group after all the discussion 
and voting is done with? Or does this mean another round of voting and
discussion? 

Hiroki Morizono
Department of Biochemistry
University of Minnesota
hiroki@limerick.cbs.umn.edu
From: tim@ccwf.cc.utexas.edu
Newsgroups: bionet.general
Subject: Re: bionet.bionette or bionet.women ?
Date: 3 Sep 92 05:28:56 GMT
Organization: The University of Texas at Austin, Austin TX

In article <3805@fcs280s.ncifcrf.gov> pnh@fcsparc6.ncifcrf.gov (Paul N Hengen) writes:

>> With the exception of one open post, Una could be making those numbers up.
>> Why are there 14 offline expressions of opinions to two online?  

> ...I trust her; don't we all?

Hmmm ...  if analysis of the {Marilyn vos Savant/Monty Hall/Let's Make a Deal}
problem is used as a benchmark for assessing skill at manipulating numbers,
then perhaps not ...   :)