HDTenEightyP/NetNews huggingface dataset:
From: eric@bcserv.wustl.edu (Hugo (Eric))
Newsgroups: bionet.software
Subject: JCAMP format and software to analyze spectra
Summary: Does anyone know of public domain spectral analysis software
Keywords: JCAMP spectra
Date: 21 Nov 92 17:31:09 GMT
Organization: Washington University in Saint Louis, MO USA
NNTP-Posting-Host: bcserv.wustl.edu

Dear Netters,
     Does anyone know of an ftp site that might have software (Mac,
Sun, or MSDOS) for analyzing or at least converting either JCAMP or
Stadtler format spectral data (Protein FTIR) to a usable format.
Any pointers would be greatly appreciated.
                                       Thanks!    Eric ;-)
-- 
  Eric R. Hugo, Postdoctoral Research Associate |eric@bcserv.wustl.edu
  Dept. of Biochemistry and Molecular Biophysics|                
  Washington University School of Medicine      |               
  Box 8231, St. Louis, MO 63110_________________| (314) 362-3342
From: ACKROYD@UTSW.BITNET
Newsgroups: bionet.software
Subject: end subscription
Date: 16 Nov 92 22:04:00 GMT
Distribution: bionet

Please discontinue my subscription. Thanks Alison Ackroyd
From: spl@ivem.ucsd.edu (Steve Lamont)
Newsgroups: bionet.software
Subject: Re: Net access from home
Date: 21 Nov 1992 02:39:32 GMT
Organization: University of Calif., San Diego/Microscopy and Imaging Resource
Distribution: bionet
NNTP-Posting-Host: ivem.ucsd.edu

In article <9211210211.AA19613@net.bio.net> CZJ@CU.NIH.GOV writes:
>Is there any way to make a computer act like it is linked to
>the network even though it is hooked to a phone line through a
>modem?

Yes.  It is called SLIP or Serial Line IP.  Ask your local networking
guru.

							spl
-- 
Steve Lamont, SciViGuy -- (619) 534-7968 -- spl@szechuan.ucsd.edu
UCSD Microscopy and Imaging Resource/UCSD Med School/La Jolla, CA 92093-0608
"Morgenstund hat Gold im Mund..."
"... wer laenger schlaeft, bleibt auch gesund!" - email private communication
From: rice@embl-heidelberg.de (Peter Rice)
Newsgroups: bionet.software
Subject: Re: New RNAfold for VAX?
Date: 18 Nov 92 17:03:13 +0100
Organization: EMBL, European Molecular Biology Laboratory

In article <zxmkr08.722024950@studserv>, zxmkr08@studserv.zdv.uni-tuebingen.de (Cornelius Krasel) writes:
> Hello BioNetters,
> 
> I am looking for an executable or Fortran source for Zuker's new RNAfold
> which is able to do suboptimal folding, for a VAXstation 4000/60.
> I AM aware that there is a version for Macs out there, but it is
> limited to 200 (?) bases (and, in addition, our VAX has more
> computing power :-). I didn't find it at the Embl (my list is from the
> 14th of Nov.), and I was  unsuccessful with Archie.

The latest release of GCG (7.2) has Zuker's suboptimal fold program, under
the name MFOLD, among the new programs.

 -----------------------------------------------------------------------------
 Peter Rice, EMBL                             | Post: Computer Group
                                              |       European Molecular
 Internet:    Peter.Rice@EMBL-Heidelberg.DE   |            Biology Laboratory
                                              |       Postfach 10-2209
 Phone:   +49-6221-387247                     |       W-6900 Heidelberg
 Fax:     +49-6221-387306                     |       Germany

 ... and occasionally price@crc.ac.uk ...
From: bosborne@INSECT.BERKELEY.EDU
Newsgroups: bionet.software
Subject: E. coli Genetic Stock Center?
Date: 20 Nov 92 18:45:36 GMT
Distribution: bionet


To the group,
Does anyone know if the E. coli Genetic Stock Center (Yale), or
its contents, can be addressed, queried, examined, by email or
by ftp?

Thank you for your attention to this matter,
Brian Osborne
bosborne@insect.berkeley.edu
From: jonesbb@BELOIT.EDU (Ben Jones)
Newsgroups: bionet.software
Subject: Re: HELP: .HQX Format for Macs
Date: 18 Nov 92 09:34:23 GMT
Distribution: bionet

>The people who run Sumex-aim anticipated that people might not already have >something to unpack a binhex file.  Binhex 4.0 is available in MACBINARY format >rather than binhex, so that you can download that and use it for unpacking >everything else.  It is located in Mac-info/utils and is named binhex4.bin.  Be >sure you download it in MacBinary format rather than binary or text.

Before I get pounced on, please disregard my previous posting.  I just
discovered that I missed one message in this discussion and the above
comment doesn't help the problem.

However, I did download Binhex4.bin successfully before I posted that
message so perhaps if you keep trying it will work sometimes.

Sorry.

Ben


Ben Jones                  BioQUEST / Department of Biology
jonesbb@beloit.edu         Beloit College, Beloit, Wisconsin
From: cherry@OPAL.MGH.HARVARD.EDU
Newsgroups: bionet.software
Subject: Re: New RNAfold for VAX?
Date: 18 Nov 92 14:12:34 GMT
Reply-To: cherry@OPAL.MGH.HARVARD.EDU
Organization: Molecular Biology - Mass Gen Hospital

>In article <zxmkr08.722024950@studserv>, zxmkr08@studserv.zdv.uni-tuebingen.de (Cornelius Krasel) writes:
>>I am looking for an executable or Fortran source for Zuker's new RNAfold
>>which is able to do suboptimal folding, for a VAXstation 4000/60.
>>I AM aware that there is a version for Macs out there, but it is
>>limited to 200 (?) bases (and, in addition, our VAX has more
>>computing power :-).

The Zuker program, called MFOLD, LRNA or version 2, which does
suboptimal folding and includes Doug Turner's dangle energies can be
retrieved via anonymous ftp from these two sites:

Amber.MGH.Harvard.EDU in the VAX directory. The MFOLD.BCK is a VMS
BACKUP saveset.

FTP.Bio.Indiana.EDU in the molbio/rnafold directory. The MFOLD.BCK is
a VMS BACKUP saveset.


This version of Zuker's folding program has also just been included in
GCG version 7.2, at least the VMS version of GCG. This means it now
has a better interface and documentation.

Mike
From: kristoff@net.bio.net (David Kristofferson)
Newsgroups: bionet.software
Subject: Re: Net access from home
Date: 21 Nov 92 18:23:47 GMT
Distribution: bionet
Organization: BIOSCI International Newsgroups for Biology

> For MSDos computers, I haven't enough experience to give advice.  I believe
> there may be free slip client software though.

I saw a recent posting in comp.sys.ibm.pc.misc mentioning that the
public domain NCSA Telnet program for the PC now has SLIP capability,
but that there have been a lot of bugs reported in it.  Other than
that, I am sure that, if one wants to find more info, posting to that
USENET forum would get an answer.

Dave
From: cherry@OPAL.MGH.HARVARD.EDU
Newsgroups: bionet.software
Subject: Re: Net access from home
Date: 22 Nov 92 15:04:58 GMT
Reply-To: cherry@OPAL.MGH.HARVARD.EDU
Distribution: bionet
Organization: Molecular Biology - Mass Gen Hospital

SLIP provides TCP/IP connections through a modem connection. Many Unix
systems include SLIP software however as with many Unix administration
tasks this requires a little experience to setup. Many people are using
terminal servers that provide SLIP.  This has many advantages and can
be more easily controlled centrally. Commercial providers of Internet
connections are available in most parts of the US. There is also a
usenet group alt.internet.access.wanted for those looking for a
commercial network provider solution.

For Macintoshes you can use AppleTalk Remote Access. If you are
already using MacTCP at work then ARA and MacTCP will provide you all
the services you use at work via a modem. Several companies are
producing special devices that connect to an AppleTalk network and a
modem to provide a standalone ARA dialin connection. We use the Shiva
LanRover/L which works great.  We have full access to all AppleTalk
services plus the home Macs can be Internet nodes. A few of the
terminal server vendors are working on including ARA support within
their produces.  I have also heard there are software solutions for
Unix and VMS systems where you call into a normal fast modem and run
software on your host computer to get ARA function.  ARA and
LanRover/L are both commercial products that can be obtained from most
mail order companies.

For all these network dialin connections I'd recommend a V.32bis modem
which is 14,400 baud. These modems are available starting around ~$300
mail order.

Mike Cherry
cherry@frodo.mgh.harvard.edu
From: bsh@MED.PITT.EDU (Basavaraju Shankarappa)
Newsgroups: bionet.software
Subject: public domain software
Date: 15 Nov 92 17:51:12 GMT
Distribution: bionet

Hi netters:

	Sometime back I had posted a request on info about the availabilit
of public domain software for de-fragmenting the disk.  I thank everyone 
who made suggestions to me on this behalf.  Many of you also indicated
that I will be better off buying this kind of software as it is worth the
small amount of money it costs.  In this regard I would like to explain the
reason for my preference to public domain software.  To make one thing clear,
I am not opposed to paying money for a product/idea which someone has worked
hard at.  In my case, the reason for my request was to see that I can get 
the program in as short a time as possible.  If I have to go through the 
University bureacracy, I will have to wait for atleast 15-20 days.  
I hope I have been able to make my position more clear.
Thanks for putting up with me. '

Raj Shankarappa
Univ of Pittsburgh
bsh@med.pitt.edu
From: scott@phylo.life.uiuc.edu (Snooky Fudge)
Subject: Re: Where to get NCSA gel reader?
Organization: University of Illinois at Urbana
Date: Tue, 17 Nov 1992 15:00:18 GMT

ftp zaphod.ncsa.uiuc.edu

A DOS version does not exist.
TIFF is not supported.
--
Coffee Facts from Dr. Science:
1) You can never brew coffee too strong.
2) You can never drink too much coffee.
3) Coffee does not make you nervous.  Your own inadequacies do that.
   Coffee merely increases your perception of your own inadequacies.
4) Tea is to coffee as ginger ale is to Scotch.
From: dbigwood@LOCUS.NALUSDA.GOV (Doug Bigwood)
Newsgroups: bionet.software
Subject: Re: Net access from home
Date: 21 Nov 92 15:25:16 GMT
Distribution: bionet

PC-NFS, available from Sun Microsystems, has the option of using
SLIP which "gives a PC running PC-NFS access to remote systems and
networks through direct wiring or by telephone and modem."  I have
no personal experience with SLIP, but we use PC-NFS and are
quite happy with it.

--------------------------------------------------------------------------
Douglas W. Bigwood, Ph.D.		
Database Manager		
Plant Genome Data and Information Center
USDA, NAL, ISD				
10301 Baltmore Blvd.			
Beltsville, MD 20705			Internet: dbigwood@nalusda.gov
--------------------------------------------------------------------------
From: huff@mcclb0.med.nyu.edu (Edward J. Huff)
Newsgroups: bionet.software
Subject: Re: GratefulMed over tcp/ip???? for Mac!!!
Date: 16 Nov 92 21:50:05 GMT
Followup-To: bionet.software
Organization: NYU Chemistry Dept.

In article <zxmkr08.721510798@studserv>,
zxmkr08@studserv.zdv.uni-tuebingen.de (Cornelius Krasel) wrote:
> To my knowledge, MacTCP is NOT in the public domain. You can ftp it
> nevertheless; if you get an Eudora Package somewhere, it is included.

Apple is thinking about changing the pricing of MacTCP, so that
individual copies will be about $70 per machine, and the site
license (which was very reasonably priced) will last only a year
and cost more.  (This rumor from the author of Eudora).  NYU has
a site license for MacTCP and uses many copies.  U. Illinois has
a distribution license to distribute MacTCP for use by the Eudora
application only.  (You violate that license if you then use MacTCP
for other things...)

Anyway, to the point:  MacTCP does NOT let you access Medline
via the Grateful Med interface.  You have to have a Mac application
program that uses MacTCP.  (e.g. Eudora, NewsWatcher, XferIT, etc.
are all Mac applications that use and depend on MacTCP).  Is there
a Grateful Med application program that uses MacTCP?

--
Edward J. Huff   huff@mcclb0.med.nyu.edu   (212)998-8465
Keck Laboratory for Biomolecular Imaging
NYU Chemistry Deptartment, 31 Washington Place, New York NY 10003
Posted from the new Mac NewsWatcher 1.3d5
Newsgroups: bionet.software
From: raja@mayo.edu (Raja Muthupillai, BIR Grad Student, Dr. Robb)
Subject: request for info on resources
Reply-To: raja@mayo.edu
Organization: Mayo Foundation
Date: Sun, 15 Nov 92 23:43:16 GMT

Keywords: 


Hi,

I am new to the newsgroups in the field of molecular biology.
I am very much interested in the resources availble in the network,
for researchers in molecular biology.  I'd greatly appreciate any
relevant information, like  major ftp sites, softwares available, etc

If anyone wants to send it directly, please do so.
My email address  is raja@mayo.edu

Thanks,
Raja.
From: gustilo@POBOX.UPENN.EDU
Newsgroups: bionet.software
Subject: Comments Wanted -- MathCad 2.5
Date: 19 Nov 1992 11:54:51 -0600
Organization: UTexas Mail-to-News Gateway
NNTP-Posting-Host: cs.utexas.edu

greetings,

how suitable is this program for curve fitting?

I would like to be able to do linear, quadratic, semi-log, log-log,
log-logit and 4-parameter logistic curve fitting to name a few.

What is the quality of the resulting plots?

thanks in advance

Standard Disclaimer: 
    I am not responsible for comments that I make after 3:00 a.m. or after
5 cups of coffee, whichever comes first.
From: mike@chi.uwa.edu.au (Mike Schon-Hegrad)
Newsgroups: bionet.software
Subject: Whereabouts of GratefulMed (TCP) for the Mac??
Date: 18 Nov 92 04:24:24 GMT
Organization: Western Australian Research Institute for Child Health
NNTP-Posting-Host: andrew.chi.uwa.edu.au
X-UserAgent: Nuntius v1.1.1d12
X-XXMessage-ID: <A72FE6760101E03A@andrew.chi.uwa.edu.au>
X-XXDate: Wed, 18 Nov 92 04:24:22 GMT

I'm sorry if I've missed this already, I was following the thread for a
while then didn't read news for a week.

Could someone please email me (and reply to the group for the benefit of
others) as regards whether a version of GratefulMed for the Mac using TCP
does exist, and where we can FTP it from if that is possible.

Many thanks

MIKE
_________________________________________________
Mike Schon-Hegrad
Research Officer

Western Australian Research Institute for Child Health
Roberts Road, SUBIACO				
Western Australia    6008

Phone	(09) 340 8388
Fax	(09) 388 3414
email	mike@chi.uwa.edu.au     
__________________________________________________
Organization: University of Maine System
Date: Thursday, 19 Nov 1992 08:32:45 EST
From: Robert Roxby <RROXBY@MAINE.MAINE.EDU>
Newsgroups: bionet.software
Subject: Where is PGEN (primer design) prog?

There is a DOS program called PGEN for PCR primer design available
somewhere by anonymous ftp.  I had it, but lost it in a little
hard disk fiasco.  I will appreciate it if you can help me
to find it again.  Thanks, Robert
Newsgroups: bionet.software
From: JANIEMI@FINABO.ABO.FI (Jarmo Niemi TUY)
Subject: T-tracking program ?
Organization: Abo Akademi University, Finland
Date: Sat, 21 Nov 1992 15:50:23 GMT
X-News-Reader: VMS NEWS 1.24

	I am looking for a program, that enables finding the
	location of clones in a DNA sequence by the results of T-tracking
	(running only one sequencing reaction / clone)

	I am doing a sequencing project by the shotgun sequencing
	approach, and to identify clones that would enable filling
	gaps in the second strand sequence, would like to find a
	program to do the above. I am using the gel assembly
	system of GCG, so anything compatible with it would be perfect.

Jarmo Niemi   Biochemistry, University of Turku
              SF-20500 Turku, Finland
              ++358-21-6335758
              janiemi@finabo.abo.fi

"You may quote me"
	-this sentence
		(quoted from Douglas R. Hofstadter:Metamagical themas)
			{therein reprinted from Scientific American,
			January, 1981}
				[and probably published even before]
From: harper@convex.csc.FI (Rob Harper)
Newsgroups: bionet.software
Subject: Re: Where to get NCSA gel reader?
Date: 17 Nov 92 11:22:28 GMT
Organization: Finnish Academic and Research Network Project - FUNET

In <9211170816.AA22514@halogene.genethon.fr> pouliot@GENETHON.GENETHON.FR (Yannick Pouliot) writes:

>Fellow biospacers, these are probably FAQs but here goes: Where can one FTP NCSA gel reader? Is there a DOS version? Can it read TIF or TIFF files?

Here is a clip of a link from our gopher at finsun.csc.fi
I have a directory of different FTP sites that you can explore
NCSA is one of them.

Name=GelReader
Type=1
Port=70
Path=ftp:ftp.ncsa.uiuc.edu@/Mac/GelReader/
Host=finsun.csc.fi

If you don't have gopher and waht to do it the hard way then ftp to
ftp.ncsa.uiuc.edu and login as anonymous then cd to /Mac/GelReader

RGDS -=ROB=-


--
 ~ Rob Harper                    ~ E-mail:          harper@convex.csc.fi    
 ~ Finnish State Computer Centre ~ Molbio/software: harper@nic.funet.fi
 ~ P.O. Box 40                   ~ Telephone:       +358 0 457 2076
 ~ SF-02101 Espoo Finland        ~ Fax:             +358 0 457 2302
From: CZJ@CU.NIH.GOV
Newsgroups: bionet.software
Subject: Net access from home
Date: 21 Nov 92 01:39:02 GMT
Distribution: bionet

Is there any way to make a computer act like it is linked to
the network even though it is hooked to a phone line through a
modem?

Background:  My office computer is linked to the net through our LAN.
I have become hooked using gopher and all of the other tools
Dave Kristofferson has been preaching about.

The problem is that the only time I have to really work with my computer
is at home in the evening.  The computer I log into from home
is on the net (helix@nih.gov) and supports high speed modem connections.
The price of 9,600 baud modems has come down to the point where
I can afford to buy one.

So now I am relegated to dialing in to helix, using the helix gopher server,
or FTPing to other sites, transfering files back to helix,
and then KERMITTING them back to my PC.  Ugh.

It owuld seem much better to use the PC version of gopher, somehow
hook into helix through a modem but somehow mimic a network
connection.

Am I dreaming or is this realistic?

Jim Cassatt
From: mzhang@XIBALBA.CSHL.ORG (Michael Zhang)
Newsgroups: bionet.software
Subject: public domain games?
Date: 16 Nov 92 13:36:57 GMT
Distribution: bionet

Hi netters:
Are there any public domain games or children educational softwares?
M.Zhang
mzhang@cshl.org
From: khofmann@biomed.biolan.uni-koeln.de
Subject: Re: Program for alignment with "boxes" ?
Reply-To: khofmann@biomed.biolan.uni-koeln.de
Organization: Biochemical Institute, Cologne University
Distribution: bionet
Date: Mon, 23 Nov 92 10:42:24 GMT

In article <1992Nov21.120846.17648@gserv1.dl.ac.uk>, Roman.Jerala@IJS.si writes:
>Hallo netters, 
>does anybody know of a program which, when given as input alignment of several 
>sequences, adds boxes around aminoacids when more than ?% are equal (as you can
>often see in publcations). I would prefer version for PC or SGI and ftp-able 
>programs.

You could try BOXSHADE. It is available by FTP from
BIOMED.BIOLAN.UNI-KOELN.DE and a couple of other ftp-servers.
There are versions for VAX/VMS and for MSDOS.

Best Regards,
               Kay
From: GUNNELL@FCRFV2.NCIFCRF.GOV (Mark A. Gunnell)
Newsgroups: bionet.software
Subject: RE: Wanted: DNAStar info (Mac vers)
Date: 16 Nov 92 20:16:01 GMT
Distribution: bionet

Carolyn -

> A researcher here has asked me to reap the Net Wisdom with regard to the 
> Mac DNA sequencing program DNAStar (aka LaserGene?). He's interested in
> finding out its capabilities, usefulness, and any pros/cons - especially
> in comparison with GeneWorks.

  I don't have any personal experience with the package myself, but there
is an abbreviated review in the November 1 issue of Genetic Engineering News,
page 6.  The reviewer, Kevin Ahern, indicates a more substantial review will 
appear in Biotechnology Software (a series of reviews beginning with the Nov.
/Dec. '92 issue).

-Mark
-------------------------------------------------------------------------------
Mark A. Gunnell                   | Internet: gunnell@ncifcrf.gov
Sci. Applications Analyst         | Bitnet:   gunnell%ncifcrf.gov@cunyvm.bitnet
Biomedical Supercomputer Center   | Phone:   (301) 846-5779
PRI/DynCorp                       |
NCI-FCRDC                         |
PO Box B, Bldg 430                |
Frederick, MD 21702-1201  USA     |
-------------------------------------------------------------------------------
From: 00arcarmicha@leo.bsuvc.bsu.edu
Newsgroups: bionet.software
Subject: MacInTax/Peachtree
Date: 17 Nov 92 17:39:01 GMT
Organization: Ball State University, Muncie, In - Univ. Computing Svc's





        I AM CURRENTLY PART OF GROUP WHO IS WORKING TO AUTOMATE A SMALL
    ACCOUNTING FIRM AND WE HAVE DECIDED ON TWO SOFTWARED PACKAGES THEY
    ARE
                     MacInTax
                     Peachtree Insight
        DOES ANYONE HAVE ANY COMMENTS OR FAMILIAR WITH THESE PACKAGES AND
    IF SO, PLEASE REPLY TO ME DIRECTLY, I WOULD APPRECIATE IT.
From: stonger@point.cs.uwm.edu (Kelly Stonger)
Newsgroups: bionet.software
Subject: Thesis topic
Date: 15 Nov 92 18:15:48 GMT
Distribution: usa
Organization: University of Wisconsin, Milwaukee
NNTP-Posting-Host: 129.89.2.5





Hi,

I am a graduate student in computer science and I am looking for
a masters thesis topic. Since I also have a masters in microbiology,
I would like to work on a topic that relates to both computer science
and biology (such as RNA folding or DNA sequencing). Can you
recommend any research topics in this (or any other) area that I
can use as a basis for a thesis. Any help would be greatly
appreciated.


K. Stonger
From: kupiec@mail1.ciwemb.edu (Bill Kupiec)
Newsgroups: bionet.software
Subject: Grateful Med-Macintosh
Date: 18 Nov 92 07:43:23 GMT
Distribution: bionet
Original-To: Bio Software <bio-software@uk.ac.daresbury>


                                                              Time:7:32 AM
Subject:     Grateful Med-Macintosh                           Date:11/18/92
A TCP version of Grateful Med for the Macintosh currently does NOT exist.
According to the National Library of Medicine's newsletter this month, an
Internet access version of Grateful Med is expected to be released in early
1993. For DOS users, the Internet version is now available (it is version 6.0).

- Bill
*------------------------------------------------------------*
Bill Kupiec
kupiec@mail1.ciwemb.edu, AppleLink: KUPIEC
Computer Systems Manager, Carnegie Institution of Washington
*------------------------------------------------------------*
From: nholford@ccu1.aukuni.ac.nz (Nick Holford)
Newsgroups: bionet.software
Subject: Paperchase? How can I access it? (Boston/Beth Israel)
Date: 15 Nov 92 20:17:01 GMT
Organization: University of Auckland, New Zealand.

I have heard that there is a database of clinical trials under the name
Paperchase. It originates from Beth Israel Hospital clinical computing I
think. Can anyone tell me more about it and how I can access it?

-- 

Nick Holford, Dept Pharmacology & Clinical Pharmacology
University of Auckland, Auckland, New Zealand
INTERNET: n.holford@aukuni.ac.nz
Newsgroups: bionet.software