HDTenEightyP/NetNews huggingface dataset:
From: cherry@OPAL.MGH.HARVARD.EDU
Newsgroups: bionet.software
Subject: Re: Genbank FASTA server -> NCBI?
Date: 1 Oct 92 04:54:36 GMT
Reply-To: cherry@OPAL.MGH.HARVARD.EDU
Organization: Molecular Biology - Mass Gen Hospital

>In article <28SEP199211032524@seqvax.caltech.edu>, mathog@seqvax.caltech.edu (David Mathog) writes:
>>Dennis Benson's reply to my post:
>>>  The primary reason is machine resources.  We have BLAST running
>>>  on a parallelized version of an 8-processor Silicon Graphics.
>>>  This provides very rapid turn-around for searches and allows us
>>>  to handle the daily load of between 1000 and 2000 searches per
>>>  day, including hundreds of BLASTX and TBLASTN searches which are
>>>  heavily CPU-intensive.  We simply would not have the capacity to
>>>  accommodate FASTA searches in addition to this machine load and
>>>  still provide reasonable response times.
>>
>>Here we go again.  In the bad old days we ran local FASTA's on our
>>VAXstation.  Then we offloaded these jobs to the Genbank FASTA server.

I saw nothing in your message about why you do not use the BLAST
server.

For about the last year BLAST searches have all but replaced FASTA
searches here at Massachusetts General Hospital. I don't have any
problem with the FASTA server going away because we didn't use it and
a great alternative is available (blast@ncbi.nlm.nih.gov).

I think you greatly underestimate the amount of horsepower required to
setup one of these servers. FASTA takes a lot of CPU time.  Opening a
mail server requires that you can provide and support the service for
the future.

Mike Cherry 

P.S. I also think your economics of computer purchases is flawed.  Any
computers or periferals that are purchases are used for much more that
just sequence searches. Plus in the example of a lab buying a CD-ROM
drive there are several other diskes that are available and quite
useful. In some cases not available via any other media: eg. the NCBI
Entrez CD-ROM, PIR Atlas disk and some hardware vendors routinely
provide software updates on CD.
From: zxmkr08@mailserv.zdv.uni-tuebingen.de (Cornelius Krasel)
Subject: Sequence film scanning systems?
Organization: Comp. Center (ZDV) U of Tuebingen, FRG
Date: Mon, 28 Sep 1992 14:27:09 GMT

Hello netters,

our lab is pondering about buying a scanner to evaluate DNA
sequence films. Before spending huge amounts of money :-)
I would be very happy if you would share your experiences
with some of my colleagues who are very sceptical about
BioNet. Thus I would be glad if you'd response by
email (since those colleagues don't have a Usenet access)
to hashemol@mpib-tuebingen.mpg.dbp.de.

In particular we would be interested if we should buy
a specialized system (such as advertised by IntelliGenetics
in a recent Nature issue) or if things could be worked
out with a scanner and some additional software.

Software may be Mac- or PC-based.

Thanks in advance, Cornelius.
--
/* Cornelius Krasel, Department of Physiological Chemistry, U Tuebingen    */ 
/* email: krasel@mailserv.zdv.uni-tuebingen.de (Internet)                  */
/*        krasel@chemie.uni-tuebingen.dbp.de (WIN/X400)                    */
/* "People are DNA's way of making more DNA." (anonymous)                  */
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Newsgroups: bionet.software
Subject: Re: Biocomputing Departments
Date: 30 Sep 92 17:32:01 GMT
Distribution: na
Organization: Frederick Cancer Research and Development Center

> Can we have an informal survey of the various
>"biocomputing facilities" on the net?

There is a facility here with a Cray YMP, two vax, about 20 sun workstations, a
convex and a multiprocessor (masspar?), and a staff of about 30(?) people.  It
serves researchers for molecular modelling and molecular biology for the
Frederick Cancer Research and Development Center.  Time on the cray is
available to outside researchers.

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
From: mzhang@XIBALBA.CSHL.ORG (Michael Zhang)
Newsgroups: bionet.software
Subject: fission yeast exon recognition
Date: 28 Sep 92 14:59:52 GMT
Distribution: bionet

Dear Bionetters,
I am working on a program which can be used to detect Introns from
a fission yeast genomic DNA sequence. I am collecting new (nuclear
protein coding) gene sequences. If anyone, who have just sequenced
a new gene, would like to locate the introns, please send me the
seqnece to me at: mzhang@cshl.org and I'll be glad to analyize it.
			Michael Zhang
			Cold Spring Harbor Lab.
			Cold Spring, NY 11724
From: D31@TRANAVM1.EARN (suleyman aydin)
Newsgroups: bionet.software
Subject: Biocomputing units, but just imaginary
Date: 28 Sep 92 19:12:13 GMT
Distribution: bionet
Original-To: BIO-SOFT@UK.AC.DARESBURY


 
Yes, almost the same in this corner of the world also..
 
One man is giving (actually trying to give) service to a research
centre plus being a consultant of network  besides of his ph.d.
work and mice + rats feeding..  (yes, its easy to guess, isnt it?)
 
But whats worse, I can visualise the openening gap between networkers
and the non-networkers, but the non-networkers are not even aware of
the distance... pity..
 
Nowadays, I am in hope to have a terminal in my pharmacology lab.
I wish I have enough luck..
 
suleyman aydin (ph.d. student of pharmacology)
d31@tranavm1.bitnet
Newsgroups: bionet.software
From: mrl775@tigger.jvnc.net
Subject: Re: GCG7 to Paup translation? (A)
Followup-To: bionet.software
Reply-To: mrl775@tigger.jvnc.net
Organization: TheNews 
Date: Tue, 6 Oct 1992 13:44:14 GMT

whoops...

just noticed that there is an internet address for swofford..

daveswof@vmd.cso.uiuc.edu

later,

Keith
Newsgroups: bionet.software
From: danj@chablis.gwu.edu (Dan Jacobson )
Subject: Re: Paup
Originator: danj@merlot.gwu.edu
Organization: George Washington University, Washington, D.C.
Date: Fri, 2 Oct 1992 21:33:08 GMT


A question was asked about the availibility of the PUAP phylogeny
package.  Paup is commercial, though the last I heard a great price
~$50 (US).  As such it is not (*should not*) be on any ftp server.

You might want to contact the author of Puap:

David L. Swofford                 Phone:    (217)244-6959
Illinois Natural History Survey   FAX:      (217)333-4949
607 E. Peabody Drive              BITNET:   DAVESWOF@UIUCVMD
Champaign, Illinois 61820 USA     Internet: swofford@uxh.cso.uiuc.edu


If you're doing phylogeny you might want to take a look at PHYLIP
by Joe Felsenstein.  Phylip is also a suite of programs for phylogeny
but is free, at a ftp site near you and comes with LOTS of documentation.



Best of luck,


Dan Jacobson


danj@chablis.gwu.edu

NOTE: My email address has changed to danj@chablis.gwu.edu, I am no longer
      danj@welchgate.welch.jhu.edu.
From: Davison@UH.EDU (Dan Davison)
Newsgroups: bionet.software
Subject: Re: Genbank FASTA server -> NCBI?
Date: 29 Sep 92 20:06:12 GMT
Distribution: bionet



And I will join Daniel Zabetakis and David Mathog in protesting the
loss of the FASTA server, for all the people that have, and are going
to, complain (just) to me about it...

I do appreciate and understand the position NCBI is in, but
arrangements could have been made before this.  

And, just think, when IRX goes away, the messages we're going to see
for months in this newsgroup about "where did IRX go"...sigh.


dan
-- 
dr. dan davison/dept. of biochemical and biophysical sciences/univ. of
Houston/4800 Calhoun/Houston,TX 77204-5934/davison@uh.edu/DAVISON@UHOU

-----RIP Isaac Asimov 1920-1992     I'll miss him --------------------

Disclaimer: As always, I speak only for myself, and, usually, only to
myself.

Newsgroups: bionet.software
From: moxness@leland.Stanford.EDU (Michael Moxness)
Subject: quantitative analysis on scanned gels
Organization: DSG, Stanford University, CA 94305, USA
Date: Fri, 2 Oct 92 00:17:08 GMT

We recently bought a desktop scanner and the Quantiscan program from Biosoft.
The scanner works great to get images of protein gels and autoradiograms, but
Quantiscan is the worst piece of software that I have ever seen.  We have
had major problems with the peak picking and integration. We are going to
return the software but would like to find another software package that can
serve our purposes.  We need to quantitate bands from the image in both 
dimensions, output gel lane plot profiles, and some sort of peak picking would
be a nice luxury, not to mention gaussian fits.  I have downloaded Image and
it seems to be a very nice program, but it is limited in the size of images it 
can handle.  I was wondering if there is anything else
out there that will be even better. Am I being too greedy? Ideally, it
would run on a DOS 386 machine but either a Mac or Sparc station version would
be OK also.  And of course the cheaper the better.

Sorry if this has been discussed recently, but I just started reading this
newsgroup.  If you could direct me to a faq file, I would be grateful.

Mike Moxness
moxness@bogart.stanford.edu

PS  The Artiscan scanner with slidescan kit has worked out well for us and it
only cost about $1800.
From: kristoff@net.bio.net (David Kristofferson)
Newsgroups: bionet.software
Subject: Re: NCBI FASTA mail server
Date: 5 Oct 92 20:26:16 GMT
Organization: BIOSCI International Newsgroups for Biology

GERLACHJ@QUCDN.QueensU.CA (Jim Gerlach - Cancer Research Labs) writes:

>I have a couple of questions about the transfer of services:

>1. Is it still possible to submit sequences by E-mail using AUTHORIN?

Yes, nothing has changed in this regards as Paul Gilna explains.
IntelliGenetics is continuing to distribute and support the Authorin
program and Los Alamos is continuing to accept Authorin submissions as
before.

>2. Are there any plans to implement IRX (or is it already available)?
>
>3. Are there any plans to implement BLAZE searches (although I realize
>   this involved private companies)?

I assume that these questions are inquiring as to NCBI's plans so they
would have to comment on that.  These services continue to be
available on a commercial basis as has been mentioned previously in
this forum.

				Sincerely,

				Dave Kristofferson
				BIOSCI/bionet Manager

				kristoff@net.bio.net
From: bchtantw@nuscc.nus.sg (Dr Tan Tin Wee)
Subject: Prophet integrated sw - comments?
Organization: National University of Singapore
Date: Sat, 3 Oct 1992 12:49:35 GMT

Dear Bionetters,

I have recently come across the software package Prophet.
From the initial description, it seems like a nicely integrated
package that stretches across many biological subdisciplines
including molbio, stats, graphics display etc.  It claims to
be easily maintained and expanded to incorporate new software.
Our problem has been that our users have to use a diverse range
of software, often on different platforms DOS, Mac and Unix,
in order to achieve their goal.  This package sounds very promising.

Has anyone had experience with this?i

Any comments on this software will be much appreciated, as we
are considering purchase as the licence is $150! any catch?
Of course, we will have to get Suns and Sparcstations to our
users, who currently are running 286 and 386s! - tall order that..

Thanks in advance.

Tin-Wee.

bchtantw@nuscc.nus.sg
Dept of Biochemistry, Natl Univ of Singapore

-- 
    Tin-Wee TAN                        /  INTERNET: bchtantw@nuscc.nus.sg
    Dept of Biochemistry               /  BITNET:   BCHTANTW@NUSVM
    National University of Singapore   /  Tel:      (65)-772-3678
    Singapore 0511                     /  Fax:      (65)-779-1453
From: lipman@void.nlm.nih.gov (David Lipman)
Newsgroups: bionet.software
Subject: NCBI FASTA mail server
Date: 5 Oct 92 16:19:12 GMT
Organization: National Library of Medicine
X-Newsreader: Tin 1.1 PL4


communications to NCBI, it's clear that there is definite interest in
having a NCBI FASTA mailserver.  We had initially decided to forgo this
because of the demands on resources, and because, as mentioned by M.
Cherry, we had been making BLAST available to a number of sites on an
experimental basis and had not received explicit feedback regarding the
need for additional access to FASTA.  Bill Pearson has generously
agreed to modify FASTA so that it can read the file format we use
centrally for sequence searching (this same format will be available on
CDROM's updated every 2 months starting in February).  Thanks to Bill's
work, the single format will avoid the need for another copy of all the
sequence data on our BLAST server.

When this software is available and tested we'll put the FASTA server
up for public access and announce the availability via the bulletin
boards and in the header messages of our e-mail servers.  The priority
of these searches will probably be lower than BLAST searches due to
their greater requirements for CPU cycles.

Supporting additional computational tools makes real demands on our
resources and have to be balanced by significant gains in
functionality.  For example, I'm not convinced that FASTN searches are
really worth adding -- although they result in alignments with gaps,
they are unlikely to yield matches that would not be found with
BLASTN.  In order to detect significant nucleic acid similarities in
such large databases requires fairly strong similarity (coding or
non-coding) and these non-gapped regions would be found with BLASTN.
This, of course, is arguable and your input is appreciated.

We will be doing our best to continue to upgrade the sequence searching
facilities at NCBI, incorporating new computational approaches developed
at NCBI and from researchers around the world.  Suggestions are welcome!

Thanks,
David Lipman
NCBI
From: robison1@husc10.harvard.edu (Keith Robison)
Newsgroups: bionet.software
Subject: UNIX Scripts for NCBI Sequence Server
Date: 6 Oct 92 04:44:41 GMT


	I'm posting the following in the hope that someone
will find it useful.  The new NCBI server is quite powerful,
but often too much so.  Many routine queries yield far more
entries than desired, due to the failure to remember to 
properly restrict the search.  I have come up with the following
two shell scripts to reduce this problem in my daily work.
To use them, make the listed addition to your .mailrc file and
then follow the instructions in the header of each script.
	Execute a "chmod +x" command on each script, put
them on your $path, and you will be ready to go.  If you often
retrieve GenBank entries by accession number, just adapt fetch2 -- 
change [LOC] to [ACC].

Keith Robison
Harvard University
Department of Cellular & Developmental Biology
Department of Genetics / HHMI

robison@ribo.harvard.edu 



# First, add the following line to your .mailrc file
alias ncbifetch retrieve@ncbi.nlm.nih.gov

#fetch -- general retrieval script
#         first argument is database name
#Usage: fetch database locus1 locus2...
set $*
rm -f gpf
touch gpf
echo "DATALIB " $1 >>gpf
echo "BEGIN" >>gpf
while [ $# -gt 0 ]
 do
     echo '"' $1 '" [LOC]' >>gpf     
     shift
 done
mail ncbifetch <gpf
rm gpf

#fetch2 -- retriever for specific database
#          create one version for each database (i.e. gpfetch, swfetch)
#          replace !!!! with correct database name
#Usage: gpfetch locus1 locus2...
set $*
rm -f gpf
touch gpf
echo "DATALIB !!!!" >>gpf
echo "BEGIN" >>gpf
while [ $# -gt 0 ]
 do
     echo '"' $1 '" [LOC]' >>gpf     
     shift
 done
mail ncbifetch <gpf
rm gpf
From: Fuchs@EMBL-Heidelberg.DE (Rainer Fuchs)
Newsgroups: bionet.software
Subject: Bug fix in MacPattern v2.0.1
Date: 2 Oct 92 16:29:12 GMT
Followup-To: bionet.software
Organization: EMBL Data Library

I just discovered a memory allocation problem in MacPattern v2.0.
For BLOCKS searches, if the input sequence was less than 60 residues
long, MacPattern would run out of memory quickly.
This bug is fixed in v2.0.1.

MacPattern is a Macintosh application for protein sequence analysis
using the PROSITE and BLOCKS databases and for the identification
of statistically significant specific protein segments.

MacPattern can be obtained 

1) by electronic mail from netserv@embl-heidelberg.de:
   Get Mac_Software:macpattern.hqx

2) by anonymous ftp from ftp.embl-heidelberg.de:
   /pub/software/mac/macpattern.hqx

3) by electronic mail from the author (fuchs@embl-heidelberg.de)

4) on floppy disk from the author:
   Rainer Fuchs, EMBL Data Library, Postfach 10.2209, W-6900 Heidelberg,

Rainer Fuchs
EMBL Data Library
Fuchs@EMBL-Heidelberg.DE
From: WAGNERF@BRUNB.BITNET (Wagner Fontes)
Newsgroups: bionet.software
Subject: Multi-task software
Date: 26 Sep 92 22:21:57 GMT
Distribution: bionet

Ron Henderson writes:
>======================================================================== 28
>Message-Id: <9209251645.AA21815@genbank.bio.net>
>To: bio-soft@genbank.bio.net
>From: rhh2h@fulton.seas.Virginia.EDU (Ron Henderson)
>Subject: WANTED:  non-windows software to get PC to multitask
>Date: 25 Sep 92 15:50:41 GMT
>Sender: usenet@murdoch.acc.Virginia.EDU
>
>I have heard that software packages exist to allow one to run two
>sessions at once on an IBM compatible PC.  I think a control sequence
>is used to alternate between the two sessions.
>
>Does anyone have information about such software. (I have a 286).
>
>--
>Ron Henderson                Internet:  rhh2h@Virginia.EDU
>EE PhD student               BITNET  :  rhh2h@VIRGINIA
>THN C237                     UUCPNet :  ...!uunet!virginia!rhh2h
>University of Virginia       Voice   : " HEY Ron!! "
>

Dear Ron:

       The best solution for you would be Microsoft Windows. The latest
version (3.1) runs in your 286, but... (slower, much less ability to handle
memory and disk, etc...). I would try it, but if you are planning to use
it for hard tasks, you'd better consider an upgrade to 386 or 486.

       There is also another software called Multilink. This will enable
your computer to run multi-task or multi-user modes. I used the first
version of the software 10 years ago in a IBM PC (8088). Sorry, but I
don't know if it is still available nor the distributor's name.

Wagner Fontes
Brazilian Center of Protein Sequencing
Biochemistry & Protein Chemistry Lab.
University of Brasilia - Brazil
E-Mail WAGNERF AT BRUNB
From: Keith.A.Johnson@DARTMOUTH.EDU
Newsgroups: bionet.software
Subject: blaze
Date: 2 Oct 92 00:57:59 GMT
Distribution: bionet

I haven't been paying strict attention to some of the more recent postings on
the database search programs and the ftp names now in use.  I was wondering
if there is a site available for BLAZE searches as there is for the BLAST
searches?  I have had a bad experience with a BLAST search and received more
believable information from the BLAZE algorithm.

Thanks
Keith Johnson
From: danp@POGO.CBS.UMN.EDU ("Dan S. Prestridge")
Newsgroups: bionet.software
Subject: Biocomputing Depts.
Date: 28 Sep 92 14:47:57 GMT
Distribution: bionet



In reply to Keith Elliston's biocomputing facilities survey:

  I think such a survey would be a great idea. The results of such a 
survey could help substantially with planning, justification, funding,
and staffing. In addition it would be nice to know who is out there, 
what they are doing, and how they are doing it. I think this definitely
has newsgroup potential.

-dan

___________________________________________________________________________
Dan S. Prestridge, Ph.D.			E-mail: DANP@MOLBIO.UMN.EDU
Director					Telephone: (612) 625-3744
Molecular Biology Computing Center (MBCC)       Fax: (612) 625-5780
Department of Biochemistry
University of Minnesota
1479 Gortner Ave.
St. Paul,  MN  55108
___________________________________________________________________________
From: updatets@ray.nlm.nih.gov (Test account for LANL Update@genome.lanl.gov)
Newsgroups: bionet.software
Subject: Re: Genbank FASTA server -> NCBI?
Date: 26 Sep 92 07:49:52 GMT
Distribution: usa
Organization: National Library of Medicine
X-Newsreader: Tin 1.1 PL4

mathog@seqvax.caltech.edu (David Mathog) writes:
: Is the NCBI going to continue the Genbank Fasta e-mail server?

David,

  NCBI plans to provide only the BLAST programs (BLASTN, BLASTP,
  BLASTX, and TBLASTN) on an e-mail server.  The BLAST server's
  address is:  blast@ncbi.nlm.nih.gov  (The word 'help' in the
  body of a message to this address will retrieve documentation
  on using the server.)
: 
: If yes, could someone please post the details?
: 
: If no, why not?

  The primary reason is machine resources.  We have BLAST running
  on a parallelized version of an 8-processor Silicon Graphics.
  This provides very rapid turn-around for searches and allows us
  to handle the daily load of between 1000 and 2000 searches per
  day, including hundreds of BLASTX and TBLASTN searches which are
  heavily CPU-intensive.  We simply would not have the capacity to
  accommodate FASTA searches in addition to this machine load and
  still provide reasonable response times.

  Besides the EMBL FASTA server that Dave Kristofferson mentioned,
  there is a server in Japan at the following address:

      flat-netserv@smlab.eg.gunma-u.ac.jp

  We also plan to make the sequence data, organized for sequence
  similarity searching, available on a separate CD-ROM with 
  the FASTA program included (thanks to assistance from Bill
  Pearson) for PCs and Macs.  We expect to offer this through the Govt.
  Printing Office by the end of the year.


  Regards,
  Dennis Benson
  NCBI


: 
: Thanks,
: 
: David Mathog
: mathog@seqvax.caltech.edu
: manager, sequence analysis facility, biology division, Caltech
From: GERLACHJ@QUCDN.QueensU.CA (Jim Gerlach - Cancer Research Labs)
Newsgroups: bionet.software
Subject: Re: NCBI FASTA mail server
Date: 5 Oct 92 18:41:16 GMT
Organization: Queen's University

In article <1992Oct5.162255.10184@nlm.nih.gov> lipman@void.nlm.nih.gov (David Lipman) writes:

>We will be doing our best to continue to upgrade the sequence searching
>facilities at NCBI, incorporating new computational approaches developed
>at NCBI and from researchers around the world.  Suggestions are welcome!
>
>Thanks,
>David Lipman
>NCBI

I have a couple of questions about the transfer of services:

1. Is it still possible to submit sequences by E-mail using AUTHORIN?

2. Are there any plans to implement IRX (or is it already available)?

3. Are there any plans to implement BLAZE searches (although I realize
   this involved private companies)?

Thanx for any info.

Cheers,
Jim
---
Jim Gerlach - Cancer Research Laboratories                                      
James.H.Gerlach@QueensU.CA                    Queen's University                
GERLACHJ@QUCDN.QueensU.CA (NetNorth/BITNET)   Room A309A, Botterell Hall        
tel (613) 545-6446                            Kingston, Ontario                 
fax (613) 545-6830                            CANADA  K7L 3N6
From: PARSONS_A@snd01.pcr.co.uk
Newsgroups: bionet.software
Subject: BLAZE gone in a puff of smoke?
Date: 30 Sep 92 11:19:29 GMT
Distribution: bionet
Original-To: BIO-SOFT <BIO-SOFT@UK.AC.DARESBURY>

Hi BioNetFolk,

I posted a BLAZE search to genbank.bio.net only to recieve a permission denied
message from the daemon?  Is this because of the termination of the contract 
with GenBank.  If so - does any one else know where I can find a BLAZE server?

Tony P.

Dr.Tony Parsons,	   VOX   : + 44 304 616871
Pfizer Central Research,   Internet   : parsons_a@snd01.pcr.co.uk
Ramsgate Road,             Compuserve : 100064,765
Sandwich,                "I love California, I practically grew up in Phoenix"
KENT CT13 9NJ UK          Vice President Dan Quayle
From: jds@uctvax.uct.ac.za
Newsgroups: bionet.software
Subject: tRNA searching software
Date: 28 Sep 92 12:26:06 +0200
Organization: University of Cape Town

Hello,

Could someone recommend MS-DOS or VMS based software that searches
sequence data for tRNA sequences?  Obviously free or shareware from
an FTP site would be preferred.

Thanks

Joe Santangelo   (Joe@micro.uct.ac.za)