HDTenEightyP/NetNews huggingface dataset:
From: dab@ray.nlm.nih.gov (Dennis Benson)
Newsgroups: bionet.general
Subject: Re: Question: What are the HGML numbers in Medline?
Date: 13 Apr 92 19:10:29 GMT
Organization: National Library of Medicine

steffen@mbir.bcm.tmc.edu (David Steffen) writes:
: 
: Sorry for the cross posting; looking over the list of bionet groups,
: none of them seemed all that approriate, though these seemed close.
: 
: In the Medline database are listed accession numbers for Genbank,
: EMBL, DDBJ, PIR, and HGML.*   I know what the first four are, but am
: having trouble with the fifth.  I am under the impression that HGML
: stands for Human Genome Map Locus, and that the HGML organization is
: presently GDB (Genome Data Base) at Johns Hopkins (Welch Lab), on
: which I have an account.  However, poring over the manual, and roving
: the database, I can see nowhere that the HGML numbers are used.  These
: are NOT the OMIM numbers, which I understand.
: 
: So... does anyone know what the HGML numbers are and how they can be
: used?


  You've just encountered an obsolete piece of data -- HGML stands for Human
  Gene Mapping Library, a database that used to be at Yale and was succeeded
  by GDB.  Several years ago, when NLM started entering cross-references to
  sequence data bases, the HGML literature references were mapped to Medline
  citations.  Since this type of change to Medline will be done in batch mode, the
  references probably will stay in Medline until the next update cycle which
  will be in November.  Til then, about the only information the HGML tag 
  communicates is that the paper referred in some way to a gene map.


  Dennis Benson
  NCBI/NLM
Newsgroups: bionet.general
From: holder@cse.uta.edu (Larry Holder)
Subject: Structural Databases
Organization: Computer Science & Engineering, Univ. of Texas at Arlington
Date: Wed, 15 Apr 1992 21:36:58 GMT

We are looking for databases to be used for testing an intelligent
structural data analysis tool.  The database should be structural or a
flat representation of a structural environment (e.g., coordinates of
3d entities).  The database will be converted to a graph
representation for input to the system.  Any pointers to such
databases would be appreciated.

Thank you.

-- 
Larry Holder (holder@cse.uta.edu)

University of Texas at Arlington, Department of Computer Science Engineering
Box 19015, Arlington, TX 76019-0015, Phone: 817-273-2596, FAX: 817-273-2548
From: kristoff@genbank.bio.net (David Kristofferson)
Newsgroups: bionet.general
Subject: Re: Image processing newsgroup under discussion
Date: 17 Apr 92 04:12:18 GMT
Article-I.D.: genbank.Apr.16.21.12.18.1992.23748
Distribution: bionet
Organization: GenBank Online Service

young@sasquatch.serum.kodak.com (Rich Young (x37176)) writes:

>	Is bionet.plants live yet?  I remember the voting, but my newsreader
>	hasn't yet asked me to subscribe.

I just announced the vote on Wednesday.  It won hands down and will be
established in the next couple of weeks.  There is one last delay
involving the reorganization of our mailing lists from IRLEARN to
Daresbury.  All of this was announced in detail on
BIONEWS/bionet.announce.

				Sincerely,

				Dave Kristofferson
				GenBank Manager

				kristoff@genbank.bio.net
From: ajharmar@castle.ed.ac.uk (A J Harmar)
Newsgroups: bionet.general
Subject: Medullary thyroid carcinoma cell lines
Summary: Looking for a source of medullary thyroid carcinoma cell lines
Date: 8 Apr 92 09:42:26 GMT
Distribution: bionet
Organization: Edinburgh University

We are looking source of medullary thyroid carcinoma cell lines. Three
such lines are available from the ATCC (American Type Culture
Collection) and we are obtaining these. However, at least one of these,
a rat cell line called 6-23, is proving problematic to grow. We would
appreciate help from other laboratories that might be able to provide us
with cell lines and/or tips on culture conditions.

The lines would be used for studies on the regulation of neuropeptide
gene expression.

------------------------------------------------------------------------------

Tony Harmar
MRC Brain Metabolism Unit
Royal Edinburgh Hospital
Edinburgh EH10 5HF
Scotland

ajharmar@uk.ac.ed.castle
------------------------------------------------------------------------------
Newsgroups: bionet.general
From: laurence@cco.caltech.edu (Dustin Lee Laurence)
Subject: Re: CALL FOR DISCUSSION: bionet.biology.used-equipment
Organization: California Institute of Technology, Pasadena
Distribution: bionet
Date: Fri, 10 Apr 1992 21:57:20 GMT

kristoff@GENBANK.BIO.NET (Dave Kristofferson) writes:


>> Why not call the group   --  bionet.equipment.recycle  -- ? 

>I used bionet.biology.used-equipment to make it clear that this was
>for biologists.  People browsing through USENET do not always put two
>and two together and realize that bionet refers to biology.  Witness
>the occasional postings of jobs on bionet.jobs which are way off in
>left field.  bionet.equipment.recycle has a "holistic aura" to it (at
>least in my little mind) that would probably attract ads for used
>psychic pyramids 8-).

But would private individuals who happen to be looking for laboratory
equipment be able to use this group?


-- 
Dustin Laurence            "Someone please stop me, before I net again."

laurence@alice.wonderland.caltech.edu
From: kristoff@genbank.bio.net (David Kristofferson)
Newsgroups: bionet.general
Subject: SNAFU is over 8-) & Important Announcement Coming.
Date: 14 Apr 92 20:06:13 GMT
Distribution: bionet
Organization: GenBank Online Service

Systems appear to be working normally finally, i.e., the transatlantic
distribution for bionet.general/BIOFORUM is now taking place via news.
We will continue to monitor this newsgroup closely though.

The BIOFORUM mailing list was shut down at GenBank from mid-day Monday
through early Tuesday AM and also at Daresbury.  If you sent in any
messages **by mail** during this period, odds are high that they were
redirected to the "bit bucket," i.e., they were not distributed.
Messages posted directly into USENET news would not have been
affected.

**********************************************************************
I will be posting an important announcement on bionet.announce/BIONEWS
later this afternoon about a general BIOSCI reorganization so please
"stay tuned" to that forum.
**********************************************************************

				Sincerely,

				Dave Kristofferson
				GenBank Manager

				kristoff@genbank.bio.net
From: kristoff@GENBANK.BIO.NET (Dave Kristofferson)
Newsgroups: bionet.general
Subject: Re: CALL FOR DISCUSSION: bionet.biology.used-equipment
Date: 10 Apr 92 23:21:31 GMT
Distribution: bionet


> But would private individuals who happen to be looking for laboratory
> equipment be able to use this group?

The group would be open to everyone for non-commercial purposes.  We
just want to make sure that the name suggests what kind of postings
are appropriate.

				Sincerely,

				Dave Kristofferson
				GenBank Manager

				kristoff@genbank.bio.net
From: suter@VAX.MPIZ-KOELN.MPG.DBP.DE
Newsgroups: bionet.general
Subject: gordon conferences
Date: 8 Apr 92 23:34:49 GMT
Article-I.D.: genbank.9204090009.AA18573
Distribution: bionet


dear colleagues,

                could somebody out there e-mail or fax me the overview
of the Gordon Spring Meetings ?
Here, at the MPI in Cologne, we recieve three copies of Science (which
should contain the schedule), but one copy is missing,the other at home
with a professor, and the library March-issues did not arrive yet ! Talking
about the era of communication !

I am, meanwhile, getting a bit worried about the registration deadlines.

distressed

(clemens)

p.s. perhaps you can drop me aline before you start faxing!
fax: xx49-221-5062-213
From: kristoff@GENBANK.BIO.NET (Dave Kristofferson)
Newsgroups: bionet.general
Subject: Re: CALL FOR DISCUSSION: bionet.biology.used-equipment
Date: 10 Apr 92 02:01:46 GMT
Article-I.D.: genbank.CMM.0.90.2.702871306.kristoff
Distribution: bionet


> Why not call the group   --  bionet.equipment.recycle  -- ? 

I used bionet.biology.used-equipment to make it clear that this was
for biologists.  People browsing through USENET do not always put two
and two together and realize that bionet refers to biology.  Witness
the occasional postings of jobs on bionet.jobs which are way off in
left field.  bionet.equipment.recycle has a "holistic aura" to it (at
least in my little mind) that would probably attract ads for used
psychic pyramids 8-).

Dave
From: ajt@uk.ac.sari.rri (Tony Travis)
Newsgroups: bionet.general
Subject: Re: Image processing newsgroup under discussion
Date: 16 Apr 92 09:05:18 GMT
Distribution: bionet
Organization: SERC Daresbury Lab., Warrington, U.K.
Original-To: Confocal Microscopy List <CONFOCAL@edu.buffalo.cc.UBVM>
Original-Cc: ajt@uk.ac.sari.rri, bioforum@uk.ac.daresbury
Via: rri2.yprri; Thu, 16 Apr 92 10:05:19 BST

> There is presently a discussion going on in news.groups regarding the
> creation of a USENET newsgroup devoted to image processing.  It was
> originally proposed as comp.graphics.image-proc, but a good case is
> being made for sci.imaging, which would be a group for scientists to
> discuss their image processing problems.  From the volume of discussion,
> it looks likely to me that some such group will be created.

Why not consider posting this sort of article to the USENET bionet
hierarchy ?

I have just been active in promoting the creation of bionet.plants
where, amongst other things, we are dicussing the application of image
analysis to plant anatomy.

We had a long discussion about the relative merits of the sci.* versus
bionet.* groups and, without criticising sci.biology, we felt that the
participants of the bionet.* groups were more likely to be interested
in the academic aspects of the subject than sci.* readers with a more
general interest in the area.

> Please participate, by posting a short note such as "I would read
> sci.imaging" to news.groups, with subject line "Re: RFD for new IMAGE
> PROCESSING newsgroup".
> Some other proposed names were comp.imag-pro, comp.dsp.imaging, etc.

Please also take a look at the bionet.* groups if you take them at your site
and join in on the proposal to create bionet.microscopy which was tentatively
suggested by Mike Folsom a short while ago.  If you don't read news, you can
subscribe to BIOFORUM which is the e-mail counterpart to bionet.general.

The bionet.microscopy thread was started in response to Mike's comments
about the infrequent traffic on the CONFOCAL list :-)

> Also, a mailing list for interested people has been set up, send subscribe
> requests to image-proc-request@skyking.oce.orst.edu.  The list will
> probably be discontinued once the newsgroup is created.

There is also the MEDIMAGE list for people interested in medical
imaging and comp.ai.vision (or the VISION list) for people interested
in image analysis/pattern recognition and the 'Pixel" digest (from
Adrian Clark at Essex in the UK).

Do we *really* need another image 'processing' group ?

IMHO we need a forum for biologists to discuss confocal and wide-field
microscopy such as bionet.microscopy, not another comp.* group.

	Tony

--
   Tony Travis <ajt@uk.ac.sari.rri>   | Dr. A.J.Travis,
                                      | Rowett Research Institute,
                                      | Greenburn Road, Bucksburn, Aberdeen,
                                      | AB2 9SB. UK. tel 0224-712751
From: eesnyder@boulder.Colorado.EDU (Eric E. Snyder)
Newsgroups: bionet.general
Subject: Re: codon usage
Date: 17 Apr 92 16:30:08 GMT
Article-I.D.: beagle.eesnyder.703528208
Organization: University of Colorado, Boulder

On a related note:

Has anyone had any experience using different codon usage tables which
reflect the C + G content of the specific sequence being examined.  Since
codon usage tables are normally based on usage in genes of differing 
C + G contents, I wonder if better results might be obtained with tables 
derived from genes of specific base composition.  Does anyone have 
any thoughts on this matter?

---------------------------------------------------------------------------
TTGATTGCTAAACACTGGGCGGCGAATCAGGGTTGGGATCTGAACAAAGACGGTCAGATTCAGTTCGTACTGCTG
Eric E. Snyder                            
Department of MCD Biology              ...making feet for childrens' shoes.
University of Colorado, Boulder   
Boulder, Colorado 80309-0347
LeuIleAlaLysHisTrpAlaAlaAsnGlnGlyTrpAspLeuAsnLysAspGlyGlnIleGlnPheValLeuLeu
---------------------------------------------------------------------------
From: cliff@WATSON.IBM.COM
Newsgroups: bionet.general
Subject: Genetics and Fiction; Mathematics and Fiction
Date: 14 Apr 92 20:33:23 GMT
Distribution: bionet

I am making a list of fiction and science-fiction books
dealing with
a) Genetics
b) Mathematics

I would love to hear suggestions from you.  If possible, include
author, year, title, publisher, city.  Also include a short description.

Send suggestions to: cliff@watson.ibm.com

Example (for genetics and fiction):

Engel, A. (1988) Variant. Donald Fine: NY.
(An excellent fictional account of gene manipulation with startling
consequences for several young Russian boys.)

Example (for math and fiction):
Faidman, C. (1958) Fantasia Mathematica.  Simon and Schuster:  New York
(A book of stories and diversions all drawn from the universe of
mathematics).
Xref: sparky bionet.general:924 bionet.molbio.genome-program:39 bionet.molbio.genbank:256
From: steffen@mbir.bcm.tmc.edu (David Steffen)
Newsgroups: bionet.general,bionet.molbio.genome-program,bionet.molbio.genbank
Subject: Question: What are the HGML numbers in Medline?
Date: 11 Apr 92 22:02:23 GMT
Followup-To: bionet.general
Organization: Baylor College of Medicine, Houston, Tx


Sorry for the cross posting; looking over the list of bionet groups,
none of them seemed all that approriate, though these seemed close.

In the Medline database are listed accession numbers for Genbank,
EMBL, DDBJ, PIR, and HGML.*   I know what the first four are, but am
having trouble with the fifth.  I am under the impression that HGML
stands for Human Genome Map Locus, and that the HGML organization is
presently GDB (Genome Data Base) at Johns Hopkins (Welch Lab), on
which I have an account.  However, poring over the manual, and roving
the database, I can see nowhere that the HGML numbers are used.  These
are NOT the OMIM numbers, which I understand.

So... does anyone know what the HGML numbers are and how they can be
used?

Thanks!

===

*For those who don't know:

The numbers I am referring to are found in the MS field of Medline.

Genbank, EMBL, and DDBJ are the accession numbers for Genbank, EMBL,
and the DNA DataBase of Japan.  The actual numbers are interchangable;
you can use the DDBJ number on Genbank and get the correct sequence,
for example.

PIR are the PIR accession numbers. (There are few of these currently
in the database).


Newsgroups: bionet.general,bionet.molbio.genome-program,bionet.molbio.genbank
Subject: Question: What are the HGML numbers in Medline?
Summary: 
Followup-To: 
Distribution: world
Organization: Baylor College of Medicine, Houston, Tx
Keywords: 


Sorry for the cross posting; looking over the list of bionet groups,
none of them seemed all that approriate, though these seemed close.

In the Medline database are listed accession numbers for Genbank,
EMBL, DDBJ, PIR, and HGML.*   I know what the first four are, but am
having trouble with the fifth.  I am under the impression that HGML
stands for Human Genome Map Locus, and that the HGML organization is
presently GDB (Genome Data Base) at Johns Hopkins (Welch Lab), on
which I have an account.  However, poring over the manual, and roving
the database, I can see nowhere that the HGML numbers are used.  These
are NOT the OMIM numbers, which I understand.

So... does anyone know what the HGML numbers are and how they can be
used?

Thanks!

===

*For those who don't know:

The numbers I am referring to are found in the MS field of Medline.

Genbank, EMBL, and DDBJ are the accession numbers for Genbank, EMBL,
and the DNA DataBase of Japan.  The actual numbers are interchangable;
you can use the DDBJ number on Genbank and get the correct sequence,
for example.

PIR are the PIR accession numbers. (There are few of these currently
in the database).


-- 
David Steffen
Department of Cell Biology, Baylor College of Medicine, Houston TX 77030
Telephone = (713) 798-6655, FAX = (713) 790-0545
Internet = steffen@bcm.tmc.edu
From: AJB@DLVH.DL.AC.UK
Newsgroups: bionet.general
Subject: Test 2 of 3 Ignore
Date: 14 Apr 92 16:51:00 GMT
Distribution: bionet

GenBank BIOSCI Test. Ignore
From: kristoff@GENBANK.BIO.NET (Dave Kristofferson)
Newsgroups: bionet.general
Subject: Re: bionet.biology.used-equipment
Date: 15 Apr 92 20:01:32 GMT
Distribution: bionet

> 
> 
>         Couldn't the exchange of used equipment information be a part of the
> SCIENCE-RESOURCES newsgroup?  Resources needn't be limited exclusively to
> funding....and this may be a way, as mentioned by a previous poster, for funding
>    agencies to be made aware of the unused equipment that's "out there".
> 

This does not fit in well with future plans for the SCIENCE-RESOURCES
newsgroup.  The entire set of BIOSCI newsgroups is read by many people
at NIH so I expect that the word will get to them regardless of the
location of the posting with BIOSCI/bionet.

Dave
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Newsgroups: bionet.general
Subject: Further GenBank Complaints
Date: 8 Apr 92 22:03:01 GMT
Organization: NCI Supercomputer Facility, Frederick, MD

Now that you all think GenBank is wonderful and all problems are solved
(or about to be solved with the new transition), I would like to point out
a problem I just came across.  Two entries contain binding sites for Gal4,
K02115 has 

     misc_binding    368..384
                     /note="binding site for GAL4 (positive control  protein)

M81879 has

     misc_feature    217..233
                     /note="GAL4 site"

This means that no program can treat these the same way.  Are there no rules on
how to enter things in GenBank?  Why don't these things have NAMES?   You can't
parse notes.  (That is, no program can be smart enough to read these notes and
automatically extract the sites.)  If this kind of problem continues to be
ignored, there will be a terrible price to pay later on!

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
From: msalminen@nphi.fi
Newsgroups: bionet.general
Subject: Have a look at bionet.molbio.hiv!
Date: 16 Apr 92 12:51:24 GMT
Organization: National Public Health Institute, Finland

Hi!

Those of you who know people working with the molecular biology of HIV, please
draw their attention to the last interesting ,8-), posting in bionet.molbio.hiv

	Mika Salminen
From: capone@net.bio.genbank (Al Capone)
Newsgroups: bionet.general
Subject: Test - 2 of 3
Date: 13 Apr 92 19:01:11 GMT
Distribution: bionet
Organization: SERC Daresbury Lab., Warrington, U.K.
Original-To: bioforum@uk.ac.daresbury
Via: UK.AC.NSFNET-RELAY;  Mon, 13 Apr 92 20:15 WET (V40 at UK.AC.DARESBURY.DLGM)


Test to bioforum@daresbury.

No need to reply.

Dave Kristofferson
From: kramer@news.miami.edu (Jack Kramer)
Newsgroups: bionet.general
Subject: Re: CALL FOR DISCUSSION: bionet.biology.used-equipment
Date: 10 Apr 92 18:08:09 GMT
Distribution: bionet
Organization: University of Miami, RSMAS

In article <1992Apr9.211509.6185@midway.uchicago.edu> kps2@midway.uchicago.edu writes:
>I think this is an interesting a potentially useful forum.  However,
>one concern that I have is that much 'used' biology equipment is
>owned by a government supplying grant funds and often tightly
>regulated by university or research foundation administrations.
>How would this problem be addressed in such a forum?
> 
>Ken Scholz
>Dept. of Physiology
>Univ. of Chicago
>
>

This discussion should somehow be crossposted or forwarded to make
it available to granting agency personnel.  A great deal of used
equipment sits idle in store rooms at every campus and institution.
Most of it could continue to be very useful at other places.  The net
result could be the saving of a great deal of money by the grantors.
It seems to me that the major beneficiaries, the researchers and
the grantors, will have to squeeze the administrators in the middle
very hard, but the results would be worth it.

I would love to be able to get a commitment for the purchase of
needed equipment at reduced prices when preparing a proposal budget.
The NET could make this possible.

Perhaps some of the mid level administrators could see some advantage
to them as part of the "surveying out" of used equipment.
From: Charlotte.R.Williams@dartmouth.edu (Charlotte R. Williams)
Newsgroups: bionet.general
Subject: codon usage
Date: 17 Apr 92 13:05:30 GMT
Organization: Dartmouth College, Hanover, NH


Hello

Anyone have experience using various computer programs for the analysis
of codon usage?

Thanks--

Charlotte Williams
Dartmouth College
charlotte.williams@dartmouth.edu
From: ajt@doc.ic.ac.uk (Tony Travis)
Newsgroups: bionet.general
Subject: Re: Mechanical stress and lignification
Date: 12 Apr 92 17:31:47 GMT
Organization: Department of Computing, Imperial College, University of London, UK.

young@sasquatch.serum.kodak.com (Rich Young (x37176)) writes:
: [...]
:    I didn't think for a minute that I'd be able to contribute anything of
:    use to this group, but I just happened to be reading through back issues
:    of SCIENCE NEWS and remembered a reference to the Braam study.
: 
:    The summary is in SCIENCE NEWS, Vol. 137, No. 8, page 117; Feb. 24, 1990,
:    and the published study is in CELL, Feb. 9, 1990.
: 
:    I hope this is of some use, even though it's a week late.

Thanks for posting it Rich - this *is* useful to me and saved me having
to search for it in literature that I am unfamiliar with.

	Tony
-- 
    Tony Travis <ajt@uk.ac.sari.rri>  | Dr. A.J.Travis 
                                      | Rowett Research Institute,
                                      | Greenburn Road, Bucksburn, Aberdeen,
                                      | AB2 9SB. UK. tel 0224-712751
From: mwfolsom@hydra.unm.edu (Mike Folsom)
Newsgroups: bionet.general
Subject: Re: CALL FOR DISCUSSION: bionet.biology.used-equipment
Date: 10 Apr 92 00:47:01 GMT
Article-I.D.: lynx.jjsjhm
Distribution: bionet
Organization: University of New Mexico, Albuquerque

In article <!jsjpgm@lynx.unm.edu> mwfolsom@hydra.unm.edu (Mike Folsom) writes:
>
>Why not call the group   --  bionet.equipment.recycle  -- ? 
>Al 
>Once somebody starts using the "system" for this they might be inclined 
>to explore other groups.

Somehow this got garbled - what I meant to say was that -

Why not call the group  -- bionet.equipment.recycle -- ?

Anyway, I think that this group could be a good "draw" for bionet.
Once somebody starts using the "system" for this they might be inclined
to explore other groups.

^^^^^^^^^^^\\\\\

Oh well so much for my knowledge of the vi editor!  Try, try again.

Michael

_______________________________________________________________________________
M.W.Folsom/Biology/UNM/Albuqueerque,NM87131/505.277.4228/mwfolsom@unmvm.unm.edu