HDTenEightyP/NetNews huggingface dataset:
From: news@lerami.lerctr.org (Usenet administrator)
Subject: lerami.lerctr.org news summary for the week ending Sun Sep 13, 92
Date: Sun, 13 Sep 1992 07:31:09 GMT
Distribution: dfw
Reply-To: postmaster@lerami.lerctr.org
Organization: USENET news support, lerami.lerctr.org, Irving, TX 75060-7726
Followup-To: dfw.news



System             Accept sys% tot%    Dup sys% tot%    Rej sys%     Sent avl%
amix                    6 100%   0%      0   0%   0%      0   0%        0   0%
awful                   0   0%   0%      0   0%   0%      0   0%      337   2%
cmptrc                 32 100%   0%      0   0%   0%      0   0%     1470   7%
cnbisis                 1 100%   0%      0   0%   0%      0   0%     1703   8%
dbyrne                  0   0%   0%      0   0%   0%      0   0%     3740  18%
egsner                  0   0%   0%      0   0%   0%      0   0%       57   0%
europa                  3 100%   0%      0   0%   0%      0   0%        0   0%
lerami                326 100%   2%      0   0%   0%      0   0%        0   0%
maps                    0   0%   0%      0   0%   0%      0   0%      230   1%
mic                     0   0%   0%      0   0%   0%      0   0%       57   0%
niteowl                 0   0%   0%      0   0%   0%      0   0%      183   1%
nnbsys                  0   0%   0%      0   0%   0%      0   0%      332   2%
rwsys               20739  97%  98%    617   3% 100%      1   0%       57   0%
taoami                 10 100%   0%      0   0%   0%      0   0%     7196  34%
txsil                   2 100%   0%      0   0%   0%      0   0%     1941   9%
whitwiz                 0   0%   0%      0   0%   0%      0   0%     9364  44%
woodwrk                 0   0%   0%      0   0%   0%      0   0%      746   4%

TOTALS              21119  97%         617   3%           1   0%    27413


Categories Received               Articles
alt                                     2175
austin                                    19
bit                                      343
biz                                       64
comp                                   14644
control                                  242
dfw                                       72
expired*                                 333
gnu                                      637
houston                                    8
junk                                     101
k12                                        8
misc                                    3173
news                                     907
pubnet                                     1
rec                                     2403
sci                                      848
soc                                      424
talk                                     141
tx                                       393
vmsnet                                    22


Newsgroups: convex.news.stats,dfw.news.stats
From: usenet@news.eng.convex.com (news access account)
Subject: convex (news.eng.convex.com) NNTP summary for week ending Sat Sep 12, 92
Date: Sun, 13 Sep 1992 06:06:08 GMT
Distribution: dfw
Reply-To: usenet@news.eng.convex.com
Organization: Engineering, CONVEX Computer Corp., Richardson, Tx., USA
Followup-To: convex.news,dfw.news
X-Disclaimer: This message was written by a user at CONVEX Computer
              Corp. The opinions expressed are those of the user and
              not necessarily those of CONVEX.


NNTP peer article transfers

Article Reception (they contact us)
System               Offered   Took   Toss   Fail Toss   Elapsed     CPU    Pct
convex.convex.com     105757 102988   2769      0   3% 162:32:54   2:51:33   2%

TOTALS                105757 102988   2769      0   3% 162:32:54   2:51:33   2%

Article Transmission (we contact them)
System                 Offrd   Took   Toss   Fail  Pct   Elapsed     CPU    Pct
news.utdallas.edu      87803  35190  52613      0  60% 168:01:52   0:24:30   0%
convex.convex.com        808    215    593      0  73% 167:23:48   0:27:01   0%
maui.nrc.com           33549   2813  30735      1  92%  48:03:04   0:02:14   0%
news.oryx.com          83583  83492      0     91   0% 168:08:09   0:29:09   0%
riogrande.cs.tcu.edu   93854  93840     12      3   0% 187:49:38   0:31:52   0%
constellation.ecn.uoknor.edu
                       96264  90498   5759      7   6% 168:08:09   0:35:04   0%
news.oc.com            87389  51687  35700      1  41% 134:17:03   0:22:19   0%

TOTALS                483250 357735 125412    103  26% 1041:51:43   2:52:09   0%

Transmission Connection Attempts            ------errors-------
System                   Conn     OK     NS    Net   Rmt  Pct
news.utdallas.edu        1654   1654      0      0      0   0%
convex.convex.com         408    408      0      0      0   0%
maui.nrc.com              829    829      0      0      0   0%
news.oryx.com            1344   1344      0      0      0   0%
riogrande.cs.tcu.edu     1046   1046      0      0      0   0%
constellation.ecn.uoknor.edu
                         1311   1311      0      0      0   0%
news.oc.com              1225   1225      0      0      0   0%

TOTALS                   7817   7817      0      0      0   0%

Newsgroups: dfw.news.stats
From: uucpmgr@rowdy.lonestar.org (The Big UU Know Who)
Subject: rowdy.lonestar.org uucp summary for the week ending Sat Sep 12, 1992
Reply-To: uucpmgr@rowdy.lonestar.org
Organization: Rowdy Systems, Ft. Worth, TX, USA, 76109
Distribution: dfw
Date: Sun, 13 Sep 1992 04:53:41 GMT
Followup-To: dfw.news


Remote   -----------K-Bytes----------- ----Hours---- --Avg CPS-- --Files--
 Host         Recv      Sent     Total   Recv   Sent  Recv  Sent Recv Sent
------   --------- --------- --------- ------ ------ ----- ----- ---- ----
rwsys      47726.4    1466.9   49193.3   11.4    0.3  1191  1493 2555   27
proteus        0.6   36619.8   36620.4    0.0    6.6   205  1590    2 1980
skyler        42.4    7550.8    7593.2    0.1    9.8   184   218   18  710
qcdev         42.5    3376.3    3418.8    0.0    1.1   780   838    5  171
warell         3.5    1807.6    1811.1    0.0    2.3   151   220    8  178
jasoom         1.2       2.1       3.3    0.0    0.0   166   231    2    2

                   -------------SUMMARY-------------
                   Total active uucp sites:      6
                   Total files recv:          2590
                   Total files sent:          3068
                   Total files:               5658
                   Total hours recv:          11.5
                   Total hours sent:          20.2
                   Total hours:               31.6
                   Total K-bytes recv:      47,817
                   Total K-bytes sent:      50,823
                   Total K-bytes:           98,640
From: wl07@ns1.cc.lehigh.edu (WAI-MING LEUNG)
Newsgroups: bit.general
Subject: Testing
Date: 11 Sep 92 22:44:36 GMT
Organization: Lehigh University

I am just testing.

-- 
            "Where there is a will, there is a way."

            - Leung, wai-ming.
Newsgroups: bit.general
From: mpeters@pax.eunet.ch (MBX Michael Peters)
Subject: test
Organization: EUnet Login/Mailbox Service
X-Newsreader: Tin 1.1 PL3
Date: Sat, 5 Sep 1992 12:51:03 GMT


what? no sig??
hm...

Newsgroups: bit.general
From: mpeters@pax.eunet.ch (MBX Michael Peters)
Subject: testing..
Organization: EUnet Login/Mailbox Service
X-Newsreader: Tin 1.1 PL3
Date: Sat, 5 Sep 1992 12:14:58 GMT

Newsgroups: bit.general
From: n3robert@student.business.uwo.ca (Nigel Robertson)
Subject: Using Bitnet
Organization: University of Western Ontario
Date: Wed, 9 Sep 1992 16:12:16 GMT

I have a question.  How can I use Bitnet in Ontario to send messages to a friend living in B.C._edit


n3robert@student.business.uwo.ca (Nigel Robertson)
Western Business School  --  London, Ontario
From: jasper@vax.path.ox.ac.uk
Newsgroups: bit.listserv.info-gcg
Subject: Re: Register of GCG users
Date: 4 Sep 92 18:16:47 GMT
Organization: Oxford University Molecular Biology Data Centre
Nntp-Posting-User: jasper

In article <1992Sep4.064929.2530@nic.funet.fi>, harper@convex.csc.FI (Rob Harper) writes:
> Hello from Finland,
> 
> When I look at the gcg.log on our machine I notice that the GCG programme
> gets a fair bit of use. I can see what programmes people are using, but

Anyone else got these too? What sort of numebrs do you get? (and how many 
users do you have?)

We keep meaning to analyse ours seriously and produce a breakdown of what is
used from the package, if this were done by a number of sites the results
would make interesting reading, especially in terms of which software was most
useful, and would be helpful to add improvements too. 

(GCG version 8.0 requests show starts here :))

I know GCG do their annual circular and I understand this is useful, but does 
anyone really look at what gets run in this type of detail?

 { enhancement request..... if the accounting would add the info on program
runs that were not completed, mode in which run (interactive or batch for VMS
say) and which node they are run on (the six fold difference in speed between
our VAX 4200's and VAXStation 4000/90 is going to make the cpu seconds a bit
uninformative without this)  it would help us in looking at usage and tuning I 
think }

Any thoughts?

regards,    jasper

Jasper Rees
Oxford University Molecular Biology Data Centre

jasper@vax.path.ox.ac.uk
Comments: Gated by NETNEWS@AUVM.AMERICAN.EDU
Original_To:  JNET%"info-gcg@utoronto.bitnet"
Newsgroups: bit.listserv.info-gcg
Date:         Wed, 9 Sep 1992 12:29:00 EDT
Reply-To:     Dave Mitchell <MITCHELD@SNYSYRV1.BITNET>
              <INFO-GCG@UTORONTO.BITNET>
From:         Dave Mitchell <MITCHELD@SNYSYRV1.BITNET>
Subject:      RNA splice sites

Steve Roberts asks if GCG can identify potential splice sites.  My answer
is yes, depending somewhat on the gene and the species.  A list of known
splice junction donor and acceptor sequences from previously characterized
genes in the same species can be used to generate a consensus using the
CONSENSUS program, and the resulting .CSN files are then used with
FITCONSENSUS to search your sequence for potential donors and acceptors.
However, you will have much better luck if the general boundaries of exons can
first be identified using CODONPREFERENCE, preferably with a species-specific
codon usage table.  Some codon usage tables are present in the GCG Data
Libraries, but again you can make your own using CODONFREQUENCY.

Dave Mitchell
SUNY Health Science Center
Syracuse, NY
Newsgroups: bit.listserv.info-gcg
From: harper@convex.csc.FI (Rob Harper)
Subject: Re: Register of GCG users
Organization: Finnish Academic and Research Network Project - FUNET
Date: Sat, 5 Sep 92 19:37:29 GMT

In <1992Sep4.190423.1@vax.path.ox.ac.uk> jasper@vax.path.ox.ac.uk writes:

>There are a couple of large folders of them here, so I guess most other sites 
>have something like this, but I think Rob's form is more useful since it is 
>asked for after the users get going with software.

Well if anybody has any collected information about users at their site 
and would want to share it at an international level then I would be 
happy to make it available via gopher.

>(Hope it's in English though: your server is enough to 'finish' me off
>sometimes :)) 

The Embnet Finnish BioBox option will be in english. It is quite a simple
matter to just dump mail messages into a ELM folder, and present the folder
to gopher and it then presents all the subject lines as a spereate readable
item.

>Or collect them for your own site maybe and help Rob's overflowing mailbox to 
>turn into an overflowing gopher server.

This is a good idea, so if anybody is sitting on information, please send it to
me. I would like to collate it so that it can be used as a resource for
other GCG users.

Looking forward to hearing from you.

RGDS -=ROB=-


--
   Rob Harper                     /   E-mail:          harper@convex.csc.fi    
   Finnish State Computer Centre  /   Molbio/software: harper@nic.funet.fi
   P.O. Box 40, SF-02101 Espoo    /   Telephone:       +358 0 457 2076
   Finland                        /   Fax:             +358 0 457 2302
Newsgroups: bit.listserv.info-gcg
From: harper@convex.csc.FI (Rob Harper)
Subject: Re: Register of GCG users
Organization: Finnish Academic and Research Network Project - FUNET
Date: Mon, 7 Sep 92 07:38:16 GMT

In <1992Sep4.191647.1@vax.path.ox.ac.uk> jasper@vax.path.ox.ac.uk writes:

>Anyone else got these too? What sort of numebrs do you get? (and how many 
>users do you have?)

After I put the accounting on it has generated alot of information but it
is difficult to get any statistics out of it.
At present the GCG.LOG stands at half a mega.

-rw-rw-rw-  1 harper   csc        490220 Sep  7 10:07 GCG.LOG;1

I generated a mailing list from it with the command

cat GCG.LOG |awk '{print $1}' | sort | uniq > GCGMAIL

Now I can keep everyone who uses GCG at our site informed of new developments.
I also printed out a one month's usaage to see what programmes were being
used and how much CPU's they were using, but 25 pages of usernames, programme
names and CPU times does not make very inspiring reading.

>We keep meaning to analyse ours seriously and produce a breakdown of what is
>used from the package, if this were done by a number of sites the results
>would make interesting reading, especially in terms of which software was most
>useful, and would be helpful to add improvements too. 

Well I thought about importing it into EXEL and doing some pie charts
or histograms so as to condense the data down to something reasonable
that could be understood by the " directors". Something visual rather
than screeds of names and numbers.

>(GCG version 8.0 requests show starts here :))

It would be nice it GCG considered making some tools to take the GCG.LOG data
and make it into some presentation graphics. When it comes to justifying
your existance to the powers that be, it is best to do it in technicolor.
I would be interested to know if anybody makes use of the accounting 
obtained in the GCG.LOG, and what techniques they use to make presentation
graphics out of it.

RGDS -=ROB=-


--
   Rob Harper                     /   E-mail:          harper@convex.csc.fi    
   Finnish State Computer Centre  /   Molbio/software: harper@nic.funet.fi
   P.O. Box 40, SF-02101 Espoo    /   Telephone:       +358 0 457 2076
   Finland                        /   Fax:             +358 0 457 2302
Comments: Gated by NETNEWS@AUVM.AMERICAN.EDU
X-Delivery-Notice:  SMTP MAIL FROM does not correspond to sender.
X-Vms-Mail-To: UUCP%"info-gcg@utoronto.bitnet"
Newsgroups: bit.listserv.info-gcg
Date:         Mon, 14 Sep 1992 12:43:16 PDT
Reply-To:     farrah@IMMUNEX.WA.COM
              <INFO-GCG@UTORONTO.BITNET>
From:         farrah@IMMUNEX.WA.COM
Subject:      database access

From:	NAME: Terry Farrah
	FUNC: Protein Chemistry
	TEL: x4206                            <FARRAH AT A1 AT GENOME>
To:	UUCP%"info-gcg@utoronto.bitnet"@MRGATE


    This a question for GCG:

    Are you developing any more sophisicated tools for sequence database
    access than StringSearch and FindPatterns?  There is so much parseable
    information in the headers of GenBank, EMBL/Swiss-Prot, and PIR
    sequence entries that it is a real shame to only be able to access it
    using simple string-matching.  This is my single biggest frustration
    with the GCG package.

    And now a question for GCG users:

    What tools are you using for this purpose, other than StringSearch?
    Are there any publicly available programs that run on the VAX?  Are any
    of them GCG-compatible - i.e., they make use of GCG-formatted sequence
    files?  I saw a posting recently for Etzold's SRS (Sequence Retrieval
    System) - any others?

    Terry Farrah, Immunex Corp.  (farrah@immunex.wa.com)
Comments: Gated by NETNEWS@AUVM.AMERICAN.EDU
X-Delivery-Notice:  SMTP MAIL FROM does not correspond to sender.
X-Envelope-to: info-gcg@utoronto.bitnet
X-VMS-To: IN%"info-gcg@utoronto.bitnet"
X-VMS-Cc: LIUNI
Newsgroups: bit.listserv.info-gcg
Date:         Mon, 14 Sep 1992 13:16:00 +0200
Reply-To:     LIUNI@MVX36.CSATA.IT
              <INFO-GCG@UTORONTO.BITNET>
From:         LIUNI@MVX36.CSATA.IT
Subject:      Information on fusion protein

Hi,

can anyone help me for this problem.

  My goal is to search in eukaryotic proteins for specific amino-acids
regions whose role is to fuse two membrane structures together.
Such amino-acids sequences have already been detected and widely
studied in some viral proteins.

We have started to search these peptides by using the sequence
homology criterion, that is applying FASTP on the Swissprot database.
Yet, this strategy has not produced good results. So, maybe homology is
not the primary criterion to follow in this search.

Thus, I was wondering if there is any better method to support me in
this functional screening.

Thank you in advance.

                                               Sabino Liuni

________________________________________________________________________

   Dr. Sabino Liuni
   Research Area of CNR -Italy

   E_mail: LIUNI@MVX36.CSATA.IT
           LIUNI@IBAMARTE.BITNET
------------------------------------------------------------------------
X-Delivery-Notice:  SMTP MAIL FROM does not correspond to sender.
Priority:     normal
P1-Message-Id: DE*DBP*MPG;920915165509
X400-Trace:   DE*DBP*MPG; arrival Tue, 15 Sep 92 16:55-0100 action Relayed
X400-Trace:   de*dbp*GMD; arrival Tue, 15 Sep 92 16:55+0200 action Relayed
Newsgroups: bit.listserv.info-gcg
Date:         Tue, 15 Sep 1992 10:57:15 -0400
Reply-To:     Christoph Gartmann <gartmann@VMS.MPIIB-FREIBURG.MPG.DBP.DE>
              <INFO-GCG@UTORONTO.BITNET>
From:         Christoph Gartmann <gartmann@VMS.MPIIB-FREIBURG.MPG.DBP.DE>
Subject:      Re: Database access

>        However, XQS (like SRS if I understood correctly) DOESN'T make use
>of the GCG-formatted databases. You have to create all the index files from
>the flat databases. On my Vax, the files used by XQS take more than 140,000
>blocks (EMBL + PIR/MIPS). That's a real problem...

Wrong! SRS creates its indices from the sequences in the GCG database format.
Thus, there is no need to store sequence data twice. In addition, SRS is able
to include any other database format. Here we have EMBL & PIR together with
some smaller sequence databases (EPD, PROSITE, enzymes,...). The SRS indices
currently occupy 82336 blocks.

Regards

+-------------------------------------------------------------------------+
| Christoph Gartmann          Phone : +49-761-5108-465   Fax: -221        |
| Max-Planck-Institut fuer    PSI   : PSI%026245761030173::GARTMANN       |
| Immunbiologie               X400  : S=gartmann;OU=vms;O=mpiib-freiburg; |
| Stuebeweg 51                        P=mpg;A=dbp;C=de                    |
| D-7800  Freiburg            RFC   : gartmann%vms.mpiib-freiburg.mpg.dbp.|
| FRG                                 de@relay.cs.net                     |
+------------ Do you know MENUE, the user environment for VMS? -----------+
Comments: Gated by NETNEWS@AUVM.AMERICAN.EDU
X-Delivery-Notice:  SMTP MAIL FROM does not correspond to sender.
X-Envelope-to: info-gcg@utoronto.bitnet
Content-type: text/plain; charset=US-ASCII
X-Mailer: ELM [version 2.4beta PL12]
Mime-Version: 1.0
Content-Length: 2119
Newsgroups: bit.listserv.info-gcg
Date:         Thu, 10 Sep 1992 16:56:32 +0300
Reply-To:     Rob Harper <Rob.Harper@CSC.FI>
              <INFO-GCG@UTORONTO.BITNET>
From:         Rob Harper <Rob.Harper@CSC.FI>
Subject:      Gopher register of GCG users.

Well the respose to the request for information has not been all I expected.
Never the less there is now a register of GCG projects, which can be
accessed via gopher. Here is the clip from the first page.

If you have a gopher client then the command

gopher -pm/.BioBox/GCG_Projects convex.csc.fi 70

should let you read the entries in the register.

I would really encourage everyone to send me details of their GCG projects
to harper@convex.csc.fi

This is a great chance to be of service to each other.
Do the right thing... REGISTER. Even the moderator of the INFO-GCG
list has given details of his project. It is so easy to build up
a database like this on Gopher that it would be a shame to let this
opportunity slip just because of inertia.

               Internet Gopher Information Client v1.03

                                  GCG Projects

 -->  1.  Projects using GCG..
      2.  Leukocyte adhesion proteins (Martti Tolvanen).
      3.  Integrin adhesion (Matti Korhonen).
      4.  Gene Expression in Atherosclerosis (Timo Hiltunen).
      5.  Plant Molecular Biology (Alan Schulman).
      6.  Human Papillomavirus research (Raimo Pollanen).
      7.  Computing in Biology (Ari-Pekka Kvist).
      8.  VACUOLAR H+-ATPASE IN BONE RESORPTION (Tiina Laitala).
      9.  Gene expression of germinating barley (Ilkka Porali).
      10. Soluble starch synthaases (Jaana Tyynela).
      11. Semliki forest virus (Marko Hyv|nen).
      12. new collagens (Marko Rehn).
      13. Genetics of Metanogens (John Nash).
      14. Eukaryotic flagellar dyein ATPase  (David R. Mitchell).
      15. Signal analysis in nucleic acid sequences (Christoph Gartmann).
      16. cDNA clones/Clostridial toxins (Luis Avila).
      17. Promoter recognition/Sigma factors (Michael Lonetto).

I really do want to hear from you.

   Rob Harper                     /   E-mail:          harper@convex.csc.fi
   Finnish State Computer Centre  /   Molbio/software: harper@nic.funet.fi
   P.O. Box 40, SF-02101 Espoo    /   Telephone:       +358 0 457 2076
   Finland                        /   Fax:             +358 0 457 2302
Comments: Gated by NETNEWS@AUVM.AMERICAN.EDU
X-Delivery-Notice:  SMTP MAIL FROM does not correspond to sender.
Via:      UK.AC.MAN.CR.PICR;  9 SEP 92 16:48:38 BST
Newsgroups: bit.listserv.info-gcg
Date:         Wed, 9 Sep 1992 16:50:00 GMT
Reply-To:     Steve Roberts
              <BMCSAR@PATERSON.CHRISTIE-HOSPITAL.MANCHESTER.AC.UK>
              <INFO-GCG@UTORONTO.BITNET>
From:         Steve Roberts
              <BMCSAR@PATERSON.CHRISTIE-HOSPITAL.MANCHESTER.AC.UK>
Subject:      RNA splice sites

Greetings,

A user has just asked me if GCG can tell him the potential RNA splice sites
in his sequence. I said TFD but he said no! Is there an easy answer? Or a hard
answer?

Thanks.

Steve.

+-----------------------------------------+-----------------------------------+
|Dr Steve Roberts                         | E-Mail: BMCSAR@UK.AC.MAN.CR.PICR  |
|Paterson Institute for Cancer Research   |         bmcsar@picr.cr.man.ac.uk  |
|Christie Hospital                        |                                   |
|Manchester M20 9BX.  U.K.	  	  | Phone: 061 446 3147 (direct)      |
+-----------------------------------------+-----------------------------------+
|               Work Supported by the CANCER RESEARCH CAMPAIGN                |
+-----------------------------------------------------------------------------+
Comments: Gated by NETNEWS@AUVM.AMERICAN.EDU
X-Envelope-to: info-gcg@UTORONTO.BITNET
X-VMS-To: IN%"info-gcg@utoronto.bitnet"
Newsgroups: bit.listserv.info-gcg
Date:         Tue, 15 Sep 1992 16:35:00 GMT
Reply-To:     BIONET@FRCGM51.BITNET
              <INFO-GCG@UTORONTO.BITNET>
From:         BIONET@FRCGM51.BITNET
Subject:      Re: Database access

        I completely agree that STRINGS is some sort of precambrian
brontosaurus (makes me think of VI, still the 'standard' text editor in
UNIX!), and that an efficient retrieval system is what is missing in
GCG.
        There's been a recent posting on SRS on Bionet. I got a version by
C. Gartmann who kindly sent me a Backup, but I had no time yet to install
it.
        Here I use the XQS program from PIR/NBRF (also a posting appeared
on Bionet). Quite efficient for retrieving a sequence by keywords, author,
etc.. Not designed, however, to assemble sequences from the feature tables.
Looks very much like PSQ for those who used it. Well, I like XQS.
        However, XQS (like SRS if I understood correctly) DOESN'T make use
of the GCG-formatted databases. You have to create all the index files from
the flat databases. On my Vax, the files used by XQS take more than 140,000
blocks (EMBL + PIR/MIPS). That's a real problem...