HDTenEightyP/NetNews huggingface dataset:
From: francis@monod.Biol.McGill.CA (Francis Ouellette)
Newsgroups: bionet.general
Subject: D=2 r=2 j=1 f=0 (was: Re: class-L list?)
Date: 18 Nov 92 00:53:21 GMT
Organization: McGill University

joe@evolution.u.washington.edu (Joe Felsenstein) writes:

>>        I have the addresses: 
>>        LISTSERV@SBCCVM and CLASS-L%SBCCVM.BITNET@CUNYVM.CUNY.EDU
>>        but neither of these works from my internet site.

>I think it's  class-l@ccvm.sunysb.edu

but be sure to Email the listserv to subscribe to this group ... ;-)

rergards,

francis

--
| B.F. Francis Ouellette  
| manager, yeast chromosome I project
| dept of biology, McGill university, Montreal, Qc, Canada
| francis@monod.biol.mcgill.ca
From: cherry@OPAL.MGH.HARVARD.EDU
Newsgroups: bionet.general
Subject: Re: info request IGD database
Date: 21 Nov 92 15:02:09 GMT
Reply-To: cherry@OPAL.MGH.HARVARD.EDU
Organization: Molecular Biology - Mass Gen Hospital

>In article <1992Nov18.172914.25335@alchemy.chem.utoronto.ca>, fbignone@alchemy.chem.utoronto.ca (Franco Bignone) writes:
>>
>>I am currently looking for information about a Human Database:
>>IGD, Integrated Genomic Database, that I understand should be related
>>to the Human Genome project, does anyone have more information about it?
>>Who developed it, where is available by ftp etc.

IGD is developed at the Cancer Center in Heidelberg, Germany by Otto
Ritter.  IGD's goal is to integrate many of the current human genome
databases. IGD currently connected with GDB. Otto is also working on
using the ACEDB software for presentation of the database information
on top of a Sybase database. I'm not sure if IGD is online yet. Otto
can be reached at: dok261@cvx12.inet.dkfz-heidelberg.de

Mike Cherry
cherry@frodo.mgh.harvard.edu
From: cliff@WATSON.IBM.COM ("Cliff Pickover ", 914 945-3630)
Newsgroups: bionet.general
Subject: Offer to Represent Data in Color
Date: 17 Nov 92 14:15:30 GMT
Distribution: bionet

I am testing a data-colorizer program which converts an array of numbers
(such as in an image, microscopic or mathematical surface, etc.) to a
colored image in visually useful ways.  If you have an array of data
which you would like to represent in novel, colorful, and scientifically
or artistically useful ways, I may be able to return a slide of your
data to you after conversion by the colorizer program.  The program is
useful for revealing patterns not easily seen with simple color maps.
Please send a note to cliff@watson.ibm.com for more information.
Be sure to tell me where you're from and what your're working on.
From: amit@imtech.ernet.in (Amit Ghosh)
Newsgroups: bionet.general
Subject: Abs from Env. & Mol. Mutagenesis requested.
Date: 16 Nov 92 12:17:15 +0530
Distribution: world
Organization: Inst. of Microbial Technology, Chandigarh, India

Would somebody kindly send me the abstract of the foloowing paper:
Environmental and Molecular Mutagenesis Vol.20,1992,53-60, I do not
know the author's name nor do I have access to this Journal.I would
be thakful if this request is considered as very very urgent .
thanks,
-- 
Dr. Amit Ghosh                      Phone: +91 172 45004 x213
Institute of Microbial Technology   Email: amit@imtech.ernet.in
P O Box 1304, Sector 39A            UUCP:
Chandigarh 160 014 India.           ...!uunet!sangam!vikram!imtech!amit
Newsgroups: bionet.general
From: gwilliam@crc.ac.uk (Gary Williams x3294)
Subject: Re:  info request IGD database
Organization: MRC Human Genome Resource Centre
Date: Fri, 20 Nov 1992 10:50:02 GMT

In article <1992Nov20.020130.20960@seas.gwu.edu> danj@merlot.gwu.edu (Dan Jacobson ) writes:
>In article <1992Nov18.172914.25335@alchemy.chem.utoronto.ca> fbignone@alchemy.ch
>em.utoronto.ca (Franco Bignone) writes:
>>I am currently looking for information about a Human Database:
>>IGD, Integrated Genomic Database, that I understand should be related
>>to the Human Genome project, does anyone have more information about it?
>>Who developed it, where is available by ftp etc.
>I'm not sure but could you be thinking of the Genome Database (GDB)?

The person you should contact for more information on the IGD project
is:

Otto Ritter
DKFZ
Heidelberg
Germany
email: dok261@cvx12.inet.dkfz-heidelberg.de

The Integrated Genome Database (IGD) aims to integrate as much human
genome data as possible and graphically display it using Durbin &
Thierry-Mieg's ACeDB program. 

We have the preliminary version (IGD-FRED-ACE) set up on our system. 
The whole IGD system is still in the developmental phase, but it is
still very impressive. 

The IGD-FRED-ACE is the front-end database of the IGD.  The whole IGD
system is still in the developmental phase, and consequently the data is
not complete.  The current data held, as of June 26, 1992 is:

   Class            # of objs   Naming          Source DB(s)
   ---------------|-----------|--------------|------------
   Chromosome          24                       GDB
   Chrom_Band         625                       GDB
   Gene              2986       HGM symbols     GDB
   Locus            13838       HGM symbols     GDB
   Sequence         12436       em:<ID>         EMBL    (primate only)
                     2211       sw:<ID>         SwissProt (human only)
   Clone             4289                       RLDB(ICRF), Xq28
   Contig              18                       Xq28
   OMIM              5759       <MIM #>         OMIM
   Probe            24009       gdb:<ID_#>      GDB
                      766       dp:<ID_#>       UK DNA Probe (ICRF)
                      444       rl:<ID_#>       RLDB(ICRF)
   Clone_Grid           1                       Xq28
   Image                2                       Xq28
   ---------------------------------------------------------
   TOTAL           278,099 objects / 173 Mbytes of disk space



-- 
GARY WILLIAMS,  Computing Services Section,  Janet:       G.Williams@UK.AC.CRC
MRC-CRC & Human Genome Mapping Centre,       Internet:    G.Williams@CRC.AC.UK
Watford Rd, HARROW, Middx, HA1 3UJ, UK
Tel 081-869 3294   Fax 081-423 1275
From: cliff@WATSON.IBM.COM ("Cliff Pickover ", 914 945-3630)
Newsgroups: bionet.general
Subject: Unusual topics
Date: 17 Nov 92 17:36:27 GMT
Distribution: bionet

About a year ago, I mentioned or asked questions in this forum on some
rather strange topics, including:  the mapping of genetic sequences to
music, the coding of extraterrestrial messages in our genes, board games
played on maps of the human digestive system, board games which model
the spread of humans from hypothetical origins in Africa, robot
surgeons, fractal ant farms, simple computer simulations of the spread
of AIDS, etc. A few of you expressed interest in how these projects were
coming.  If still interested, send me a note at cliff@watson.ibm.com.

Thanks, Cliff
From: CZJ@CU.NIH.GOV
Newsgroups: bionet.general
Subject: Re:  stryder-like program for pc
Date: 23 Nov 92 16:29:16 GMT
Distribution: bionet

> could someone please direct me to a pc compatible program which
> is similar to the mac program stryder?  i.e.- one in which
> you type in a dna sequence and it shows you the restriction enzyme
> cutting sites?
>
> thanks
> -------------
>

Try seqaid from Don Roufa.  One of the modules allows you to do just
that.  Seqaid is available from the embl mail server or the
usual US FTP sites.

Jim Cassatt

Newsgroups: bionet.general
From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert)
Subject: Re: Wanted: Drosophila clones and/or sequences.
Keywords: Drosophila clones 
Organization: Biology, Indiana University - Bloomington
Date: Thu, 19 Nov 1992 13:20:46 GMT

In article <1992Nov19.004249.27962@midway.uchicago.edu> ecec@midway.uchicago.edu writes:
>We are mapping hybrid sterility genes in Drosophila and need
>to find either clones or sequences from known cytological locations.
>In particular  we are looking for "anything" in the 
>(polytene) intervals 5A - 5E  and 16D-16E.  

Those who are interested in Drosophila genetics, stocks and other info 
can find a wealth of information available over the Internet, by
using Internet Gopher to ftp.bio.indiana.edu.   We keep there
Drosophila data bases and the emerging FlyBase compendium
of Drosophila genome information.   

Thru Gopher you can search several of these databases for known cytological
locations (and other things).  There is a clone database, as maintained
by John Merriam, that may answer this particular question.  Michael Ashburner's
Flybase includes accession numbers of the sequenced Drosophila genome
linked to cytological locations.  You might also find help in the other 
data sections also.

                                   Drosophila

      1.  About Drosophila Gopher  [23Feb92, 1kb].
      2.  Clone database search <?>
      3.  Cytological features search <?>
      4.  Drosophila Archive/
      5.  Drosophila Information Newsletter <?>
      6.  Drosophila Stocks at Bloomington, USA  <?>
      7.  Drosophila Stocks at Bowling Green, USA  <?>
      8.  Drosophila Stocks at Umea, Sweden <?>
      9.  Fly people address search <?>
      10. Flybase/
      11. Flybase search  <?>
      12. Redbook/
      13. Redbook search <?>
 
                 Clone database search: 5A 5B 5C 5D 5E 16D 16E

      1.  "XR.
      2.  "4F-5A.
      3.  "4F-5A.
      4.  "5A.
      5.  "5B.
		... and many more

Here is a small selection of these search results
from the document '//Drosophila/Drosophila Archive/clonelist.txt'.

Location      Category  Subject (gene-name/ rearrangement/ markers)
                     Key       Kilobases       Reference
----------------- ----  --------------------------------------------------------
---------------      --------  -----------     ---------------------
"5A            ", CL,"satellite related repeats
                        ","1      ","0kb;0kb"      ,"DiBartolomeis:Mil"
"5B            ", RE,"T(1;3)Ubx21560.8A complex
                 ","2      ","Not Applied"  ,"Bender,Harvard   "
"5C            ", CL,"Actin 5C  Act5C   cytoplasmic actin
                    ","1,5,6  ","15kb;2kb"     ,"GenDev1:1161     "
"5D            ", CL,"ribosomal protein 7/8     rp7/8
                       ","1,6    ","17.8kb;0kb"   ,"MCB4:2643        "

-- 
Don Gilbert                                     gilbert@bio.indiana.edu
biocomputing office, biology dept., indiana univ., bloomington, in 47405
Newsgroups: bionet.general,bionet.software
From: lpcasson@phoenix.Princeton.EDU (Lawrence P. Casson)
Subject: NCBI (especially Kabat) databases
Originator: news@nimaster
Organization: Princeton University
Distribution: usa
Date: Fri, 20 Nov 1992 02:21:02 GMT

PROBLEM: I would like to retrieve complete mouse T-lymphocyte receptor
variable domain sequences, and avoid having to deal with the small
fragments that constitute many of the GenBank entries.

I'm assuming that the Kabat and Wu database is the best place to start.
In the end, I would like nucleotide sequences that are in GCG format, so
that I can use them with Amplify for the Macintosh.  File transfers by
FTP and TurboGopher are no problem, nor is uncompression or decoding of
various file types.

Is there an easy way to generate individual sequence files from the
dump files in the kabat database at NCBI?  I heard somewhere that there
was a hypercard stack that would do this, although any solution will do.

Is there a better method than downloading kabat database files?  Is it
possible to query a database service in such a way that files with
complete sequences will be returned but not those that contain only
small fragments such as D or J regions?

Thanks for any ideas and suggestions.

Larry Casson
lpcasson@phoenix.princeton.edu

Newsgroups: bionet.general
From: danj@welchgate.welch.jhu.edu (Dan Jacobson)
Subject: Re: stryder-like program for pc
Organization: Johns Hopkins Univ. Welch Medical Library
Date: Mon, 23 Nov 1992 21:43:22 GMT

In article <1992Nov23.094926.9071@ac.dal.ca> 01moo@ac.dal.ca writes:
>hello!
>
>could someone please direct me to a pc compatible program which
>is similar to the mac program stryder?  i.e.- one in which 
>you type in a dna sequence and it shows you the restriction enzyme
>cutting sites?
>
You might want to take a look at MARKER - you can ftp it from

ftp.bio.indiana.edu in the /molbio/ibmpc directory.

Here's a clip from its documentation:

MARKER is a program for creating DNA length standards and restriction frag-

ments pattern. You may either use it to create some new length standards

(from DNA you already have) or to check out the cleavage sites / digestion

pattern of any sequences.

There are some other programs which do some or all of the things that MARKER

can do. But they are much less comfortable. You'll see.



MARKER V1.0 is FREEWARE. You are not allowed to remove the Copyright infor-

mation. I'll trie to make updates every 3 to 6 months.

  - Start program from that directory by typing marker <RETURN>

  - Change to the directory where your file is saved

    (using the first five menu options)

  - ENTER filename

  - LOAD file (be sure that the filespec is correct first)

  - CHOOSE restriction enzyme(s)

  - DIGEST

  - MAKE (and print) restriction map

  - SHOW restriction fragments pattern




Best of luck,

Dan Jacobson

danj@welchgate.welch.jhu.edu
danj@chablis.gwu.edu
From: ahouse@hydra.rose.brandeis.edu (jeremy john ahouse)
Newsgroups: bionet.general
Subject: Re: class-L list?
Date: 17 Nov 92 16:05:34 GMT
Organization: Brandeis - Center for Complex Systems
X-Xxdate: Tue, 17 Nov 92 16: 07:20 GMT
X-Useragent: Nuntius v1.1.1d12

>>I am trying to subscribe to the list server called Class-L, 
>>        I have the addresses: 
>>        LISTSERV@SBCCVM and CLASS-L%SBCCVM.BITNET@CUNYVM.CUNY.EDU
>>        but neither of these works from my internet site.
>
>I think it's  class-l@ccvm.sunysb.edu

and Joe Felsenstein was correct, thank you all.
From: jonesbb@BELOIT.EDU (Ben Jones)
Newsgroups: bionet.general
Subject: (none)
Date: 17 Nov 92 02:07:55 GMT
Distribution: bionet


A couple of months ago there was a request for information about screen
capture programs for the Mac.  I chipped in advice about a utility called
Black Box, which I said was available from sumex.  Well, it wasn't on sumex
anymore, and someone emailed me directly to find out where else it might
be.  I said I'd contact him or her when I found a copy.

I found a copy in my archives, but I accidentally deleted the email message
with the address.  If the person who requested it still wants a copy,
please contact me directly.  Or anyone else, for that matter.

Ben


Ben Jones                  BioQUEST / Department of Biology
jonesbb@beloit.edu         Beloit College, Beloit, Wisconsin
From: DALTONBR@BRUNB.BITNET ("Gustavo C. Dalton")
Newsgroups: bionet.general
Subject: The world's largest living thing
Date: 20 Nov 92 01:11:42 GMT
Distribution: bionet

Dear Lenny,
The article mentioned by Erik is:

M.L.Smith, J.N.Bruhn & J.B.Anderson (1992)
The fungus Armillaria bulbosa is among the largest and oldest living
organisms.
NATURE 356: 428-431.

Enjoy it.
Gustavo
Newsgroups: bionet.general
From: stuart@cosc.canterbury.ac.nz (Stuart Ralston)
Subject: Microbial decomposition of flowers and seeds
Organization: University of Canterbury, Christchurch, NZ.
Date: Tue, 17 Nov 1992 03:40:25 GMT

This is an abstract of my Masters thesis in Environmental Science.
Is anyone else working in this area or have any information to help
me?

Flowers and seeds are produced by most plants each year and enter
the soil system at some stage.  Ungerminated seeds and flowers are
available for enzymatic attack by micro-organisms in the soil.
This study is to quantify the amount and rate of decompostion of
a range of flowers and seeds, including native species.  Weight loss,
nitrogen mineralisation and carbon dioxide loss will be monitored
during decomposition at various time, temperature and water regimes.
It is hoped that the results will help to gain an idea of the rate of
flower and seed decomposition, as well as nutrient turnover and soil
fertility.

Thanks in advance,

Delwyn Walker

c/o     \||||||/
        / o  o \           ___  ____  stuart@cosc.canterbury.ac.nz
        \ /  \ /          /__    /   /  /
         (    )          ___/   /   /__/
          \__/
Newsgroups: bionet.general
From: eboye@radium.uio.no (Erik Boye)
Subject: The world's largest living thing
Organization: University of Oslo
Date: Thu, 19 Nov 1992 09:00:32 GMT


Dear Lenny,

An article in Nature 6-9 months ago described a fungus that was claimed to be 
the world's largest living organism, by weight. It was located somewhere in the 
central U.S.A. and, naturally, was spread over an enormous area. I am sorry, I 
do not have the exact reference.

Erik
From: L.BERTSCHINGER@CGNET.COM ("L. Bertschinger, CIMMYT")
Newsgroups: bionet.general
Subject: Cereal virus newsgroup
Date: 20 Nov 92 16:52:32 GMT
Distribution: bionet

Comment: Some time ago, I sent the following message to the BIONAUTS
	 newsgroup. I am not shure whether this message went also
	 through the channels of BIOFORUM. Therfore I am sending it
	 (again?) to this newsgroup.
	 Anyway, I am looking forward to any response. In case you are
	 interested please specify briefly your particular interests,
	 i.e. why you believe that a cereal virus newsgroup would be
	 useful for you.


----- Begin message from IN%"L.BERTSCHINGER@CGNET.COM"  12-Nov-92

From:	IN%"L.BERTSCHINGER@CGNET.COM"  "L. Bertschinger, CIMMYT"    12-NOV-1992 11:02
To:	IN%"@CGNET.COM:bio-naut@net.bio.net"  "bio-naut"
CC:	
Subj:	Cereal virus usersgroup

Return-path: <@CGNET.COM:BIOSCI-REQUEST@net.bio.net>
Date: 12 Nov 1992 09:07:50 -0600 (CST)
From: "L. Bertschinger, CIMMYT" <L.BERTSCHINGER@CGNET.COM>
Subject: Cereal virus usersgroup
To: bio-naut <@CGNET.COM:bio-naut@net.bio.net>


CIMMYT may be interested in the future to electronically connect
people studying barley yellow dwarf viruses or cereal viruses in
general.

I am trying to find out how many BYDV and cereal virus researchers
are currently using BIOSCI. I am also especially interested
to know how many scientists in the developing world may have access
to these communication channels.

Please let me know if you are conducting research in this area, if
you would be interested in such a mailing list, or if you just know
of somebody who is working in this area and who may be hooked onto
e-mail.

______
L. Bertschinger
CIMMYT, Apdo Postal 6-641, 06600 Mexico, D. F., Mexico
Tels. (595) 42100/42011; Fax (595) 41069
E-mail (Internet): l.bertschinger@cgnet.com; (Cgnet): l.bertschinger


----- End forwarded message
From: lns@gnv.ifas.ufl.edu
Newsgroups: bionet.general
Subject: amber snails, Succinea sp., diet
Date: 17 Nov 92 18:52:19 GMT

Information regarding amber snails, Succinea sp., requested. What is
the diet of this critter?  Thanks.
Newsgroups: bionet.general
From: applec@pell2l19 (Clare Apple)
Subject: Medical Illustration-Biological Illustration
Keywords: illustration, textbooks, medical
Organization: Allegheny College
Date: Mon, 23 Nov 1992 23:11:09 GMT

I would like to get some information on the availability of jobs in the  
field of medical illustration, biological illustration, and life science  
textbook illustration.  Also the average wage earned would be helpful.
From: suter@VAX.MPIZ-KOELN.MPG.dbp.de
Newsgroups: bionet.general
Subject: common cold
Date: 16 Nov 92 10:46:27 GMT
Distribution: bionet
Content-Identifier: 12
Original-To: bioforum@uk.ac.daresbury
Conversion: Prohibited


Subj:	common cold
--------------------------------------------------------------------------------

dear colleagues,

what is the source of the common cold ? in origin it is a viral diseases
but my more specific questions are:   
1. can one 'catch' a cold (by running in the snow in a wet t-shirt)
2. how does this work: is the immune system weakened by the temp shock? 
   apparently, the acitivity of the white bloodcells seems to go down after
   cold shock (personal communication by someone), but doesn't the body
   temperature stay well within the 37C range ?
3. do any of you have references/ideas/suggestions on this matter?

several of my colleagues (and me also) infected ourselves at a late night
party and were AWOL for one week, suggesting that alcohol also may have 
something to do with it.

sneezing,

clemens
===============================================================================
Clemens Suter-Crazzolara, PhD
Max-Planck-Institut fuer Zuechtungsforschung
Abteilung Genetische Grundlagen der Zuechtungsforschung
Carl-von-Linne Weg 10
5000 Koeln 30
Tel. xx49-221-5062.221           fax. xx49-221-5062.21
suter@vax.mpiz-koeln.mpg.dbp.de
===============================================================================
       all job offers should include a self-addressed, stamped envelope
===============================================================================
From: ecec@quads.uchicago.edu (Eric Cabot)
Newsgroups: bionet.general
Subject: Wanted: Drosophila clones and/or sequences.
Summary: need Drosophila clones in 5A-5E and 16DE intervals
Keywords: Drosophila clones
Date: 19 Nov 92 00:42:49 GMT
Reply-To: ecec@midway.uchicago.edu
Organization: University of Chicago

We are mapping hybrid sterility genes in Drosophila and need
to find either clones or sequences from known cytological locations.
In particular  we are looking for "anything" in the 
(polytene) intervals 5A - 5E  and 16D-16E.  

Please send email responses with reply rather than follow-up 
as most people reading this group won't be interested in the answer. 

Eric L. Cabot
Dept. of Ecol. and Evol.
University of Chicago
PH: (312) 702-3234  FAX: (312) 702-3234   email: ecec@quads.uchicago.edu
-- 
=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=v=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=
    Eric Cabot                         |       "Non Nobis Nati Solum" 
ecec@midway.uchicago.edu               | 
=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=v=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=
Newsgroups: bionet.general
From: darrenp@cs.monash.edu.au (Daz)
Subject: Re: info request IGD database
Organization: Monash University, Melb., Australia.
Date: Mon, 23 Nov 1992 02:37:47 GMT

fbignone@alchemy.chem.utoronto.ca (Franco Bignone) writes:


>I am currently looking for information about a Human Database:
>IGD, Integrated Genomic Database, that I understand should be related
>to the Human Genome project, does anyone have more information about it?
>Who developed it, where is available by ftp etc.
>Tx
I saw a presentation on it at a conference in Chester - he demoed the
Integrated Genome Database. The person I spoke to was Otto Ritter at
the DKFZ (Deutsches Krebsforschungszentrum)
Im Neuenheimer Feld 280
D-6900 Heildeberg, Germany.

I don't have an email address handy - and would appreciate one if you
locate it. If you want the whole database, ftp isn't the way to go.
It was over 200Mb when I spoke to him.

Hope this helps,
--
Darren Platt, Department of Computer Science
darrenp@dibbler.cs.monash.edu.au
Monash University, Clayton Melbourne, Victoria, Australia
From: 01moo@ac.dal.ca
Newsgroups: bionet.general
Subject: stryder-like program for pc
Date: 23 Nov 92 09:49:26 -0400
Organization: Dalhousie University, Halifax, Nova Scotia, Canada

hello!

could someone please direct me to a pc compatible program which
is similar to the mac program stryder?  i.e.- one in which 
you type in a dna sequence and it shows you the restriction enzyme
cutting sites?

thanks
-------------
Chris Nguan               o__     ___     -wuz that a           o__     ___   
nguan@ug.cs.dal.ca       _.>/ _    ____      log or a          _.>/ _    ----
cow2771@ac.dal.ca       (_) \(_)                dog??         (_) \(_)     
 ,-~'`^`'~*-,._.,-*~'`^`'~*-,\|/,-*~'`^`'~ \|/ ,._.,_*~'`^`'~*-,._.,-*~'`^`'~