HDTenEightyP/NetNews huggingface dataset:
From: kristoff@genbank.bio.net (David Kristofferson)
Newsgroups: bionet.software,bionet.molbio.genbank
Subject: Re: whatswithblaze?
Date: 23 Jul 92 23:54:53 GMT
Organization: GenBank Online Service

francis@monod.Biol.McGill.CA (Francis Ouellette) writes:

>news@netnews.upenn.edu (USENET News System) writes:

>>In article <BrspLs.9wB@news.cso.uiuc.edu>,
>>brett_lindenbach@qms1.life.uiuc.edu (brett lindenbach) wrote:
>>> 
>>> The other day I received e-mail from genbank with a release announcement
>>> of BLAZE 1.0, a MP database similarity searcher. This message instructed
>>> me to write back for a help file. As of yet, I have not received any reply
>>> to my requests. Does anyone have this info? 
>>>      Much obliged,
>>>              Brett Lindenbach


>>There was a posting on the bionet.molbio.genbank newsgroup about the queue
>>software for BLAZE being swamped by all the submissions.

>maybe this is what caused genbank.bio.net to crash ...  ;-)

Not really; for that you can thank our local utility district.  We had
a disk crash yesterday which resulted from a power outage, and it took
some time to get a new disk and restore all of the files.

The Solbourne computer, genbank.bio.net, does no calculations or
queuing for the blaze server; it simply passes mail on to another
machine which front-ends the Maspar machine.  Anything sent to
blaze@genbank.bio.net yesterday simply sat in your local mail queue
until the genbank machine came back up yesterday evening.  At that
point **everything** came flooding back in to genbank.bio.net, so all
of the queues here (not just blaze, but also FASTA, retrieve, blast,
news, regular e-mail) were overloaded again.  At this time (4:45 PM
Pacific time) there are still 62 FASTA DNA searches queued and 16
FASTA protein searches queued on genbank.bio.net among other things,
so your patience is appreciated while the system reequilibrates (or,
more accurately, returns to "steady" state).  It is possible that,
under the resulting rapid influx to the blaze queue again, some jobs
may have fallen into the bit bucket.  However, I'd appreciate it if we
had a "breather" until tomorrow, Friday, before everyone starts
resubmitting supposedly lost jobs again.

				Sincerely,

				Dave Kristofferson
				GenBank Manager

				kristoff@genbank.bio.net
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Newsgroups: bionet.software
Subject: Re: Unix compiled "Primer"
Date: 21 Jul 92 15:47:15 GMT
Distribution: bionet
Organization: Frederick Cancer Research and Development Center

In article <920720175441.17af@COMB1.COMB.UMD.EDU> WWARREN@COMB1.COMB.UMD.EDU writes:

>Is there anyone out there who has compiled The Lander Labs "Primer"
>program on a Unix platform and are willing to encode it and
>Email it to me ? Please only offers at this stage.

>Bill Warren
>Ctr. Ag. Biotech.
>Univ. of Maryland

I hope I'm not misunderstanding your message.  It seems to me from your
statement that you want someone to send you a binary version of the compiled
code.  This will not necessarily work.  There are many kinds of Unix
platforms.  I have compiled this program on a Sun 4 workstation.  But if you
have a Sun 3 workstation, you could not use my binary because you have a
different machine code.  Same goes if you are running Unix on a Vax or
something else.  The beauty of Unix is that you can transport source code from
one machine to the next and compile and use it in its new location.  Just
because it is Unix does not mean that binary code is transportable.  That is
only true if the underlying machine code is the same.  (So if you have a Sparc
work station, you could use my binary, although I'm not offering!)  I suggest
that you learn to compile the code on your machine directly.  Surely you have a
C compiler!  Sorry if I misunderstood your message.

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
From: MBRCN@UK.AC.DARESBURY.DLVH
Newsgroups: bionet.software
Subject: PC Dotplot Program
Date: 27 Jul 92 19:07:00 GMT
Distribution: bionet
Original-To: BIO-SOFT@UK.AC.DARESBURY


    I have written a DOTPLOT program for PCs running MSDOS.  It requires
    EGA or VGA and incorporates Don Gilbert's ureadseq.  I have found it
    rather useful, and would appreciate it if someone would try it out and
    tell me about any bugs or improvements.  The sequence comparison is
    done in assembler, so it is quite fast.

    If anyone wants a copy of the executable, just EMAIL me at

    uk.ac.ic.ph.v1 (on JANET for UK punters)
    nsfnet-relay.ac.uk::v1.ph.ic.ac.uk::biophys (for Internet?)

    I will send a uuencoded version to anyone who manages to get an EMAIL
    message through to me.

    Ramin Nakisa,
    Biophysics Section,
    The Blackett Lab,
    Imperial College,
    London SW7 2BZ
From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert)
Newsgroups: bionet.software
Subject: Re:  Molecular Graphics on PCs
Date: 21 Jul 92 21:54:41 GMT
Distribution: bionet
Organization: Biology, Indiana University - Bloomington

In article <9207211954.AA03325@genbank.bio.net> CZJ@CU.NIH.GOV writes:
>
>You might try PCMODEL available as a shareware program.
>
>there are some real possibilities, but software is needed
>to convert the Brookhaven to PCMODEL format.  There is a hint
>that this program is available on registration ($70.00).
>  The main problem with
>the Brookhaven format is that PCMODEL requries a connect table.
>One would also like the possibility of showing only the alpha
>carbon backbone.  This could also be done with the proper manipulation
>of the Brookhaven format.  I have tried this on a 486 and
>it flies.
>

Kevin Gilbert at Indiana U (no relation to me) develops and distributes
PCMODEL (I assume it is the same PCMODEL).  He can be reached
via e-mail to Gilbert@UCS.Indiana.Edu.

I'm not overly familiar with this program.  However, Kevin does
have versions of it for MSDos-PC, Silicon Graphics, Sun, Mac,
and maybe other platforms (not VMS I think).  When I looked at
it once, Kevin was able to put PDB (Brookhaven?) format files
into it.  I don't know if this is a standard feature or something
extra.
-- 
Don Gilbert                                     gilbert@bio.indiana.edu
biocomputing office, biology dept., indiana univ., bloomington, in 47405
Newsgroups: bionet.software
From: elliston@msdrl.com (Keith Elliston)
Subject: Re: Reference Managing Program for Mac: EndNote vs. RefMan
Organization: Merck Research Laboratories
Distribution: bionet
Date: Tue, 28 Jul 92 18:01:24 GMT

gene@JMULLINS.STANFORD.EDU (Eugene Shpaer) writes:
: 
: I have been using Reference Manager (RefMan) program for several years and
: recently switched to EndNote+ (both running on Mac).
: 
: My judgement is that the EndNote is *significantly* better than RefMan.  The
: nice feature of EndNote+ is that it has so called "plug-in" module and one can
: run the program as a "tool" to Microsoft Word 5.0 (but not earlier versions).
: 
: Address: (EndNote)
: Niles & Assoc.
: 2000 Hearst Str.,
: Berkeley, CA 94709 USA
: 
: Gene
: 
: P.S. I have no association with Niles & Assoc., except as a user of their
: product.

I also use EndNote+.  I have used it since 1.0, and have found that 1.2 is 
a great product.  It lets you tailor the fields and styles to suit your needs.
I keep an extra field for the label on the reference, and place a consequetive
number in this field and stamped on my reference.  I then file all references
by this number.  I can then easily search for a key reference, look at the
label number, and pull the reference from my files.  Works very well.

It also has a very nice import function (EndLink), to import references from
MEdline and others.  I recommend it.

Keith Elliston

ps.  I too have no affiliation with Niles & Assoc..

-- 
Keith O. Elliston            elliston@msdrl.com           uunet!av8tr!elliston
AA5A/U  N9734U             elliston@mbcl.rutgers.edu     elliston@biovax.bitnet
"Beware of pseudo-experts with a mission and a grudge, especially if they are
 lawyers pretending to be scientists." -- H.W. Lewis in 'Technological Risk'
From: BIOPHYS@UK.AC.IMPERIAL.PHYSICS.VAX1
Newsgroups: bionet.software
Subject: PC Dotplot EMAIL address correction
Date: 29 Jul 92 12:40:00 GMT
Distribution: bionet
Original-To: BIO-SOFTWARE@UK.AC.DARESBURY

Whoops!  The correct email address for those not on JANET is

biophys@v1.ph.ic.ac.uk

as kindly pointed out by Martti Tolvannen.

The software is useful but still a bit rough.  All comments welcome.

In uuencoded form the entire executable and other bits occupy about 70K.
There is a readme.txt file to explain the rudiments, but if this needs
expansion, please tell me.

Ramin Nakisa,
Imperial College,
London.
Newsgroups: bionet.software
From: francis@monod.Biol.McGill.CA (Francis Ouellette)
Subject: Re: whatswithblaze?
Organization: McGill University
Date: Wed, 22 Jul 1992 21:58:54 GMT

news@netnews.upenn.edu (USENET News System) writes:

>In article <BrspLs.9wB@news.cso.uiuc.edu>,
>brett_lindenbach@qms1.life.uiuc.edu (brett lindenbach) wrote:
>> 
>> The other day I received e-mail from genbank with a release announcement
>> of BLAZE 1.0, a MP database similarity searcher. This message instructed
>> me to write back for a help file. As of yet, I have not received any reply
>> to my requests. Does anyone have this info? 
>>      Much obliged,
>>              Brett Lindenbach


>There was a posting on the bionet.molbio.genbank newsgroup about the queue
>software for BLAZE being swamped by all the submissions.

maybe this is what caused genbank.bio.net to crash ...  ;-)


francis


--
| B.F. Francis Ouellette  
| manager, yeast chromosome I project
| dept of biology, McGill university, Montreal, Qc, Canada
| francis@monod.biol.mcgill.ca
From: muriana@aclcb.purdue.edu (Peter M. Muriana)
Newsgroups: bionet.software
Subject: Scientific Documentation: Captured Video Images
Date: 22 Jul 92 19:29:23 GMT
Reply-To: muriana@aclcb.purdue.edu
Organization: Purdue University AIDS Center

Hi Netters,

I would like to get some feedback from anyone who is knowledgeable of
generating screen-captured video images.

	What is the minimal requirements needed?  A screen capture card &
	a video monitor? could you use a VCR camera?

Our department has recently purchased a high end Polaroid slide maker which
transfer computer graphic images to 35mm slide film at up to 4,000 lines
resolution/inch.  It's very nice for generating graphs, graphics, text 
slides for talks, symposia, lectures, etc.

What would be even nicer would be to capture graphic images of, say an
SDS-PAGE or DNA gel, bring it into something like Freelance, overlay text,
then generate a slide.  I know this can be done with a scanner, but the 
video capability would allow you to capture 3-dimensional objects directly 
without the need for making photos, cut & pasting them, add text, and
then re-photograph.

I know there are several companies (Fotodyne, Stratagene, etc) that have 
gel documentation/computer densitiometry systems like this, but we don't 
want the fancy software - just the basic point & capture capability to 
generate a graphic file (TIFF?) to import into a graphics software
program for addition of text, etc.

I'm sure there are others who would be interested in information of such.

Thanks in advance,
*********************************************************************
*  Peter M. Muriana, Ph.D.		Phone	= (317)-494-8284    *
*  Dept. of Food Science		FAX	= (317)-494-7953    *
*  Purdue University		E-mail	= muriana@aclcb.purdue.edu  *
*  W. Lafayette, IN  47907                                          *
*********************************************************************
From: arne@mango.mef.ki.se (Arne Elofsson)
Newsgroups: bionet.software
Subject: RE: Kinomage
Date: 29 Jul 1992 09:58:15 -0500
Organization: UTexas Mail-to-News Gateway
NNTP-Posting-Host: cs.utexas.edu

I think it was mentioned in last Prot. Science.     
that it is under development. If not
I think PC user should join forces and port
the program to Windows. I suggest that 
someone try to discuss this with the
Richardsons soon.
Arne Elofsson
From: ness@aecom.yu.edu (Seth Ness)
Newsgroups: bionet.software
Subject: animal husbandry programs
Date: 28 Jul 92 19:05:45 GMT
Distribution: bionet

does anyone know of any animal husbandry programs for the mac. 
to keep track of chimeric and transgenic mice genrations and matings with
various genotypes and phenotypes/

-- 
 Seth L. Ness                        Ness Gadol Hayah Sham          
 Ness@aecom.yu.edu
From: stoehr@embl-heidelberg.de
Newsgroups: bionet.software
Subject: Re: Accession X64346 where are you?
Date: 21 Jul 92 10:03:01 +0100
Distribution: bionet
Organization: EMBL, European Molecular Biology Laboratory

In article <1992Jul20.153618.13645@gserv1.dl.ac.uk>, PARSONS_A@uk.co.pcr.snd01
 writes:
> 
> Is accession X64346 ( a Herpesvirus saimiri virus) in GenBank or EMBL yet as I
> couldnt find it using GOS IRX?
> 
The entry is being held at EMBL until publication at the request of the
authors. If you have seen it published now, please send the citation to
update@embl-heidelberg.de (NOT to me) and the entry can be released (assuming
it is not done in the meantime).

Regards, 
Peter Stoehr
EMBL Data Library
ps sorry this is in the wrong newsgroup
Newsgroups: bionet.software
From: waite07@angis.su.oz.au ()
Subject: RNA folding programs
Reply-To: waite07@angis.su.oz.au ()
Organization: ANGIS, The University of Sydney, Australia
Date: Thu, 23 Jul 1992 08:40:10 GMT



		Dear Bionet readers,

	My lab. (Prof. R. H. Symons') has become interested in
obtaining one or more programs for the calculation and construction of
RNA secondary structures. We already have the shareware programs
"loopviewer" and "mulfold" for the Macintosh from the EMBL database
and are now looking for IBM PC compatible programs. Both shareware and
commercial programs (price is of no consideration!) are being
considered.

	My question is; can anyone give us advise as to what programs
are available and which ones are considered to be the best. 

	I realize that this question has probably been asked a number
of times and everyone is really bored with answering it, but still, I
gotta try.
	Thankyou in advance,
						Alex Jeffries
-------------------------------------------------------------------------------
Alex Jeffries
Plant Virology Lab.
Department of Plant Sciences		waite07@angis.su.oz.au (129.78.25.38)
Waite Agricultural Research Institute
The University of Adelaide		Tel.;  61  8  372 2392
South Australia
Australia
===============================================================================
Newsgroups: bionet.software
From: francis@monod.Biol.McGill.CA (Francis Ouellette)
Subject: Re: RNA folding programs
Organization: McGill University
Date: Thu, 23 Jul 1992 16:58:57 GMT

Alex Jeffrie (swaite07@angis.su.oz.au) writes:

>	My question is; can anyone give us advise as to what programs
>are available and which ones are considered to be the best. 

for the PC I know of an old one (1988 or so) called PCFOLD from Zucker et al.,
and it is available by anonymous FTP from fly.bio.indiana.edu (129.79.224.25) 
in the /ibmpc (I think) subdirectory.  From looking at the docs, I see that 
it can only handle 424 nucleotides, which is not very much.  
There is probably a better one out there, or maybe an update of this one.

At the same site in the /molbio/rnafold subdirectory there is what appears 
to be a VMS version of the same program, but I would not know what a VMS was if
it hit me on the head ...  :-) (unix is my way ...) 

>	I realize that this question has probably been asked a number
>of times and everyone is really bored with answering it, but still, I
>gotta try.

it has, but I didn't keep the answer either, and yesterday somebody was asking me
the very same question ... (sigh!)

regards,

francis


--
| B.F. Francis Ouellette  
| manager, yeast chromosome I project
| dept of biology, McGill university, Montreal, Qc, Canada
| francis@monod.biol.mcgill.ca
From: streif@vms.macc.wisc.edu (Vince Streif - MACC)
Newsgroups: bionet.software
Subject: Re: BioQuest
Date: 23 Jul 92 12:41:46 GMT
Organization: University of Wisconsin Academic Computing Center

BioQuest is alive and well.  Their schedule has been delayed somewhat by 
negotiations with publishers (they plan to release the software on CD-ROM).

I will pass Eric's message on to one of the people I know within BioQuest and
see if I can get an 'official' response to post to the group.

Vince Streif
streif@macc.wisc.edu


p.s. -- No, I'm not an official part of BioQuest.  I just happen to know
        several people who are.
From: aesmith@CALSHP.CALS.WISC.EDU
Newsgroups: bionet.software
Subject: (none)
Date: 30 Jul 92 01:03:39 GMT
Distribution: bionet

Greeting all . . .

Please excuse any cross-listing that occurs from this message as 
I have sent it out to several different nets.

The situation is this:
I have the need to translate latitude/longitude coordinants into 
easting/northing coordinants.  I have a program that completes 
the job nicely for the United States (COORDS83 ver. 1.0, Gerald 
Willis Mahun, 8616 Fairway Pl., Middleton, WI  53562), but I find 
a need for translation of Canadian coordinants (specifically Manitoba 
at the moment, but that may change by tomorrow - or perhaps it has 
already changed, I'm just unaware of it - the stuff flowing down-
hill theory you know)!

Is there, or rather, where is there a program that can do lat/long 
into easting/northing translations for Canadian locations?  I am 
extremely open to suggestions.  Please post replies directly to me, 
and I will summarize the replies I receive to the net in about a 
week or so.  We have availability to many different computers, so 
advice for programs designed for different systems will be appreciated.

Thanks in advance,

Art Smith

Wildlife Ecology Department
226 Russell Labs
University of Wisconsin-Madison
Madison, WI  53706
voice: (608) 265-2665
e-mail: aesmith@calshp.cals.wisc.edu
.



Xref: sparky bionet.software:1424 comp.binaries.ibm.pc.wanted:5151
Newsgroups: bionet.software,comp.binaries.ibm.pc.wanted
Subject: Re: REFERENCE managing program needed
From: srgxnbs@grace.dsir.govt.nz
Date: 27 Jul 92 12:05:43 +1200
Organization: DSIR, Gracefield, New Zealand

In article <1992Jul17.124725.11556@bio.vu.nl>, deboer@bio.vu.nl (Thon de Boer) writes:
> dagrawal@black.clarku.edu (Dileep Agrawal) writes:
> : I am in need of a program that can store and sort out scientific references as
> : well as download them into scientific papers in various word processors.
> : Please suggest any you know. The software can be public domain or commercial.
> : 
> There is a very nice commercial program for the Mac called EndNote plus.
> It is a database for references and can insert references in the correct format
> (for the journal of choice) and produce a list of references at the end of your
> file. It can work with most wordprocessors.
> 
> Sincerely, Thon de Boer

try AP11.ZIP in <MSDOS.DATABASE> on Simtel-20 et al, works well if a little
prinitive in some aspects

-- 
Bruce Spedding - Materials Science and Performance Group
SRGXNBS@GFV.DSIR.GOVT.NZ
Industrial Research Limited                Ph +64 +4 566-6919
 P.O.Box 31310                              Fx +64 +4 566-6004
Lower Hutt, New Zealand
From: JWALKER@EARN.SBBIOVM (jeff walker)
Newsgroups: bionet.software
Subject: leaf image analysis
Date: 28 Jul 92 16:15:06 GMT
Distribution: bionet
Original-To: bio-soft <bio-software@UK.AC.DARESBURY>

F. James Rohlf (SUNY stony brook) has two programs for fourier analysis:
 
NT-SYS (exeter publishing setauket NY) will do fourier (including elliptic
fourier) analysis.  NT-SYS costs money (??) but is well worth the price.
 
 
 
Elliptic Fourier Analysis distributed freely with the Michigan Morphometrics
software will also do the job.
 
Jeff Walker
SUNY at Stony Brook
Newsgroups: bionet.software
From: dangold1@iastate.edu (Daniel M Goldman)
Subject: Re: MSDOS mapmaker
Organization: Iowa State University, Ames IA
Date: Thu, 30 Jul 1992 13:47:33 GMT

In <1992Jul30.005659.4560@news.miami.edu> kramer@umigw.miami.edu (Jack Kramer) writes:

>Has there been any reply to the request for info on an MSDOS version
>of Mapmaker?  I have users who would also be interested.

Please include me on your list of those interested in MSDOS mapmaker
verions.  We run mapmaker on a networked UNIX system, and I would like
to cross validate the results. -DmG
From: PARSONS_A@uk.co.pcr.snd01
Newsgroups: bionet.software
Subject: Bulletin Boards for Vector Sequences
Date: 27 Jul 92 13:56:07 GMT
Distribution: bionet
Original-To: BIO-SOFT <BIO-SOFT@UK.AC.DARESBURY>

Hi Mol-Bio-Netters,

I seem to recall some companies that provided BBS access to their vector 
sequencesn (Invitrogen,Promega?).  Could some kind soul refresh my memory as to
which companies provide these services and the modem nmbers to attach to?

Many thanks,

Tony P.

 +----------------------------------------------------------------------------+
 | Dr.Tony Parsons,			VOX   : + 44 304 616871	              |
 | IT Department,			FAX   : + 44 304 616670               |
 | Pfizer Central Research,				 		      |
 | Ramsgate Road,  +----------------------   e-mail   ------------------------+
 | Sandwich,       |JANET      : parsons_a@uk.co.pcr.snd01                    |
 | KENT	           |Internet   : parsons_a@snd01.pcr.co.uk	       	      |
 | CT13 9NJ UK	   |Compuserve : 100064,765    PSImail:234216700127.parsons_a |
 +-----------------+----------------------------------------------------------+
Newsgroups: bionet.software
From: branham@binah.cc.brandeis.edu (Tom Branham, Biophysics Grad. Brandeis)
Subject: Re: Scientific Documentation: Captured Video Images
Reply-To: branham@binah.cc.brandeis.edu
Organization: Brandeis University
Date: Wed, 22 Jul 1992 22:42:54 GMT

Funny You should ask today, as I just saw a post in the scientific image
processing forum this afternoon for TimWin which is an image processing
program that also supports frame grabbing.  you do need a pc running windows
for this program, but there are others if that is a problem.  Otherwise
you will probably only need the video source (can be a camcorder, ccd,
cable or vcr) and a frame grabber (many of the new cards provide full
scale real time video support)which is likely to have software of its own
with it.  If you are looking for TimWin (and it is likely the authors could
tell you more about what you might need) You can find it at the anonymous
ftp site ftp.cica.indiana.edu and also at 130.161.189.1 (Sorry I do not
have the address for ftp.cica or the name for 130.161, but I only wrote
myself a short little note..........)  The author of this package was
ekkers@ph.tn.tudelft.nl and seemed to indicate he would like as much 
feedback as possible, so I would contact him for advice as to what might
be most apropos for what you want to do.....
                                         .....Tom Branham
From: little@ERE.UMontreal.CA (Littlejohn Tim)
Newsgroups: bionet.software
Subject: Contig assembly software- request for comments
Date: 29 Jul 92 19:13:02 GMT
Distribution: bionet.software
Organization: Universite de Montreal

Contig assembly software: request for comments 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Our group will be generating large amounts of DNA sequence
data in the near future.  We are evaluating a number of 
contig assembly programs for management of sequence projects,
but have not yet discovered one that suits our needs. 

I would be most grateful for any comments on contig assembly
software that people may have to offer.  Specifically I would
appreciate comments on:

1.	operating environment (hardware and operating system);
2.	input data format;
3.	maximum size of each gel reading;
4.	maximum size of project (length of finally assembled consensus
	sequenced);
5.	price and availability of both binary and source codes.
6.	general feelings on speed, ease of use, etc.

Thanks!  Please email me any responses; I will post a summary of replies
to the net. 


Tim Littlejohn

email: little@ere.umontreal.ca
Newsgroups: bionet.software