HDTenEightyP/NetNews huggingface dataset:
From: doelz@comp.bioz.unibas.ch (Reinhard Doelz)
Subject: Re: Mac front-end for VAX GCG
Reply-To: doelz@urz.unibas.ch
Organization: EMBnet Switzerland [BASEL]   
Distribution: bionet
Date: Fri, 6 Nov 1992 06:37:54 GMT

In article <1992Nov5.153519.15673@gserv1.dl.ac.uk>, robertson@mpib-tuebingen.mpg.dbp.de (BRAIN ROBERTSON) writes:
|> 
|> Therefore it looks pretty bad if you are trying to introdue PC users to VMS and
|> GCG. However, I have heard that a version of GCG running under Xwindows should
|> be available sometime in 1993/94. This would allow users running MacX etc to
|> access the system.

I (hopefully) will be able to get the QUERY system for public release quite 
soon. This is like the GCGNAV on UNIX but also runs on VMS. The pain with 
all these menu systems/front ends is that you need to maintain the menu 
definition langue to be quite simple. Thus, comfortable environments will 
cause a lot of overhead in maintenance (and , presumably, speed.). Second, 
who would like to start fasta with 20 clicks rather than type fasta and that's 
it? Last, don't overestimate the technology at the individual sites. Despite 
the growing 'high end' user basis, we still have the majority of our users
on serial lines. I made some attempts to run SLIP along these lines. Not 
surprisingly, X performance is moderate at best. 


-- 
+----------------------------------+-------------------------------------+
|    Dr. Reinhard Doelz            | RFC     doelz@urz.unibas.ch         |
|      Biocomputing                | DECNET  20579::48130::doelz         |
|Biozentrum der Universitaet       | X25     022846211142036::doelz      |
|   Klingelbergstrasse 70          | FAX     x41 61 261- 6760 or 267- 2078     
|     CH 4056 Basel                | TEL     x41 61 267- 2076 or 2247    |   
+------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+
               -----------------------------------------
Newsgroups: bionet.software
From: zxmkr08@studserv.zdv.uni-tuebingen.de (Cornelius Krasel)
Subject: Re: GratefulMed over tcp/ip???? for Mac!!!
Organization: Comp. Center (ZDV) U of Tuebingen, FRG
Date: Wed, 11 Nov 1992 19:39:58 GMT

In <1992Nov8.225129.15997@pollux.lu.se> Bo Servenius <Bo.Servenius@wblab.lu.se> writes:

>BTW gm6.0 is for PC isn't it??? Is there a tcp/ip version for Macs
>as well??

The TCP/IP software for Macs is MacTCP. The actual version is 1.1 (as far
as I know). I have installed it under System 7 and it works like a dream
(not like these darned IBM PCs... I always have troubles to find drivers
for our 3C507 ethernet card, e.g. to get it to work with NCSA Telnet 2.3).
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.
There is also some documentation somewhere in ftp-land about how to
configure MacTCP, but I am not sure where I picked it up ... it is
accessible via Archie, though (that was the way I found it).
--
/* Cornelius Krasel, Department of Physiological Chemistry, U Tuebingen    */ 
/* email: krasel@studserv.zdv.uni-tuebingen.de (Internet)   HAS CHANGED!!  */
/*        NO WIN/X400 MAIL POSSIBLE AT THE MOMENT!                         */
/* "People are DNA's way of making more DNA." (anonymous)                  */
From: robert@arbo.microbiol.uwa.oz.au (Robert Coelen)
Newsgroups: bionet.software
Subject: Re: GratefulMed over TCP/IP???
Date: 11 Nov 1992 08:46:19 GMT
Organization: University of Western Australia
NNTP-Posting-Host: mve.microbiol.uwa.edu.au

In article <1992Nov6.192056.23513@alw.nih.gov> donp@niaid.nih.gov (Don Preuss) writes:
>Bo.Servenius@wblab.lu.se (Bo Servenius) writes:
>
>
>Yes. Grateful Med 6.0 can work over tcpip. You can use either a version
>that works with Wollongong, or a version that works with a packet
>driver. (Uses ncsa for the engine.). I think it it somewhere around
>$25 to order it with hard copy, but it is all ftp'able from the National
                                               ^^^^^^^^^
>Library of Medicine.
>
>donp
>donp@niaid.nih.gov

Can you give us any pointers (address & directory) Don ?


Robert Coelen
Dept of Microbiology
University of Western Australia
from the Land Down Under !
From: dfenyes@thesis1.med.uth.tmc.edu (David Fenyes,ms89,,7901935)
Newsgroups: bionet.software
Subject: Looking for *nix protein/gene software
Keywords: protein dna rna analysis software
Date: 9 Nov 92 22:00:06 GMT
Organization: University of Texas Medical School at Houston

Hello *,

I'm a grad student studying the Alzheimer's beta-amyloid precursor
protein at U.T Houston, and am looking for a suite of DOS or unix-based
protein/gene analysis tools, particularly one with the capability
to read the formats used my major gene/protein databases.

I'm aware of DOS-based suites such as PC-Gene (tm), but in general
the astronomical pricing and awkward usage makes these less than
ideal.  

I'd be happy to post any information I receive.

Thanks for any info,

David
--
David Fenyes                                 dfenyes@thesis1.med.uth.tmc.edu
University of Texas Medical School           Houston, Texas
From: ksb3@cunixb.cc.columbia.edu (Katrin S Barth)
Newsgroups: bionet.software
Subject: program to identify factors binding to palindromic sequence??
Date: 10 Nov 92 16:12:19 GMT
Organization: Columbia University

Does anybody know about a program that can identify factors that bind
to a given sequence (like a palindromic sequence?)

Anukampa Barth KSB3@cunixb.cc.columbia.edu
From: CZJ@CU.NIH.GOV
Newsgroups: bionet.software
Subject: (none)
Date: 6 Nov 92 17:14:01 GMT
Distribution: bionet

Got a couple of questions for those who run gopher.

First - We are running tn3270 on a 3com network.  The gopher
client cannot access the TCP stack even though the bat files have
been properly constructed.  Our LAN manager says that the trouble
is the 3com network.  Is this correct?

Second - As an alternative I am using the gopher client that
resides on the NIH computer.  Recently the PDB announced the
establishment of a gopher that I would like to access.  Going
through the available menus it is not apparent to me how to
access a gopher hole that is not listed on the menus.  Any
advice?

Jim Cassatt
From: Mike Schon-Hegrad <mike@chi.uwa.edu.au>
Newsgroups: bionet.software
Subject: Re: GratefulMed over tcp/ip???? for Mac!!! -Ditto
Date: 11 Nov 1992 09:13:01 GMT
Organization: Western Australian Research Institute for Child Health
Distribution: world
NNTP-Posting-Host: andrew.chi.uwa.edu.au
X-UserAgent: Nuntius v1.1.1d12
X-XXMessage-ID: <A726EF9F7501E03A@andrew.chi.uwa.edu.au>
X-XXDate: Wed, 11 Nov 92 09:13:03 GMT

In article <1992Nov8.225129.15997@pollux.lu.se> Bo Servenius,
Bo.Servenius@wblab.lu.se writes:
>Thanks for your comments about gm6.0. But which is the tcp/ip adress
>where I can find it for free FTP????
>
>BTW gm6.0 is for PC isn't it??? Is there a tcp/ip version for Macs
>as well??

I would like to know this too.

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     
__________________________________________________
Newsgroups: bionet.software
From: Bo Servenius <Bo.Servenius@wblab.lu.se>
Subject: GratefulMed over tcp/ip???? for Mac!!!
Organization: Lund University, SWEDEN
X-Useragent: Nuntius v1.1
Date: Sun, 8 Nov 1992 22:51:29 GMT

Dear Netters:

Thanks for your comments about gm6.0. But which is the tcp/ip adress
where I can find it for free FTP????

BTW gm6.0 is for PC isn't it??? Is there a tcp/ip version for Macs
as well??


yours


BOSSE
Newsgroups: bionet.software
From: danj@merlot.gwu.edu (Dan Jacobson )
Subject: Re: HELP: .HQX Format for Macs
Organization: George Washington University, Washington, D.C.
Distribution: na
Date: Wed, 11 Nov 1992 18:25:52 GMT

In article <1992Nov9.190919.12960@cs.mun.ca> harold@odie.cs.mun.ca (Harold Wareham(Todd)) writes:
>I recently obtainted a Macintosh file in .HQX format from the UIBio
>archives. I need a copy of BinHex 4.0 or Stuffit to uncompress and
>use the thing. Where can I obtain copies of either of these
>programs? Thanks,
>
>- Todd

You can find Stuffit (among other places) in the util/mac directory
at IUBIO (ftp.bio.indiana.edu).


Cheers,

Dan Jacobson

danj@chablis.gwu.edu
Newsgroups: bionet.software
From: brianf@dna.uvm.edu (Brain Foley)
Subject: Re: Re: Graphing Program
Organization: Division of EMBA, University of Vermont
Distribution: bionet
Date: Wed, 11 Nov 1992 01:33:57 GMT

I have had no trouble using DeltaGraph Pro to plot 10 to the negative
power numbers.  In default mode it prints these numbers as .0001
.0000001 etc., but I can change that by selecting those data (just
click on any of these numbers and they should all get selected at
once), then changing the format of them to Scientific.

Write back if you can't figure this out.  I'm not seated at my Mac
now, so I can't give more specific instructions.
--
********************************************************************
*  Brian Foley               *     If we knew what we were doing   *
*  Molecular Genetics Dept.  *     it wouldn't be called research  *
*  University of Vermont     *                                     *
********************************************************************
From: seb1005@mbfs.bio.cam.ac.uk (Steven Brenner)
Newsgroups: bionet.software
Subject: 3D drawing software for the Macintosh
Date: 10 Nov 92 16:57:55 GMT
Organization: U. of Cambridge, England


	A member of my laboratory is interested in drawing some 3-D structures on
his macintosh. The structures need not be "perfect," so he wants something 
simple -- like a 3D version of MacDraw.  (Rather than, for example, a mac
version of autocad, etc.)

	Can anyone offer any suggestions on if there is any such software
available?

	Thanks very much

Steven Brenner
seb1005@mbfs.bio.cam.ac.uk
Newsgroups: bionet.software
From: seb1005@mbfs.bio.cam.ac.uk (Steven Brenner)
Subject: Unix Bibliography Programs?
Organization: U. of Cambridge, England
Date: Sun, 8 Nov 1992 00:23:23 GMT

I'm looking to organize the articles I've read on the computer rather than
keeping bits and pieces of references all over the place.

I've seen in the bionet archives articles about bibliography managers for the Mac
and PC, but haven't seen much discussion for Unix systems.

Can people please suggest good bibliography/reference programs?  I'll post a
summary to to the net.

Thanks very much

Steven Brenner
seb1005@mbfs.bio.cam.ac.uk
Newsgroups: bionet.software
From: scott@sklib.usask.ca
Subject: RE: (none)
Organization: University of Saskatchewan
Date: Sat, 7 Nov 1992 15:27:00 GMT

In a previous article, CZJ@CU.NIH.GOV wrote:

>Second - As an alternative I am using the gopher client that
>resides on the NIH computer.  Recently the PDB announced the
>establishment of a gopher that I would like to access.  Going
>through the available menus it is not apparent to me how to
>access a gopher hole that is not listed on the menus.  Any
>advice?

One thing you can try is to connect to the main gopher at UMN via Telnet 
to consultant.micro.umn.edu, login gopher.
Go to Other Gophers/North America/Brookhaven National Laboratory.

Then pick the link to the NIH Gopher Site.
This is defined as:

Name=NIH Gopher site
Type=1
Port=70
Path=1/
Host=helix.nih.gov


Peter Scott - Manager, Small Systems, University of Saskatchewan Libraries
                        <scott@sklib.usask.ca>
From: PARSONS_A@snd01.pcr.co.uk
Newsgroups: bionet.software
Subject: Sequence of vector Lambda gt22 anybody??
Date: 11 Nov 92 14:28:42 GMT
Distribution: bionet
Original-To: BIO-SOFT <BIO-SOFT@UK.AC.DARESBURY>

Netfolk,

I am not sure this hit the bulletin board on my last mail so here goes again...

Does anybody have or know where I can get the sequence of Lambda gt22 vector.
The reference is Jang H. Han and William J. Rutter (1987) NAR vol 15 no. 15
"Lambda gt22 an improved lamda vector for the directional cloning of 
 full-length cDNA"

Any of the other lamda variants would also be a bonus (eg gt11, gt18 etc.)

Many thanks,

Tony Parsons
 +----------------------------------------------------------------------------+
 | 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: harper@convex.csc.FI (Rob Harper)
Subject: Re: Software for PC scanners
Organization: Finnish Academic and Research Network Project - FUNET
Date: Fri, 13 Nov 92 11:53:11 GMT

In <00963814.A3D75CE0@Msu.oscs.montana.edu> uvsmr@Msu.oscs.montana.edu (Matt Rognlie) writes:

>We would like to purchase a flatbed scanner (i.e. HP ScanJet) to use
>with a DEC 486.  Is there software available which would allow us to
>use the scanner as a densitometer?  We want to scan autoradiograms or
>gels, but be able to get density data so that bands can be compared.
>Any suggestions on the latest scanner technology would also be 

This question has come up alot and there has been many responses to it
The biosci.src which is available at you local bio-gopher hole will give
you three pages of information on scanners.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% CLIP %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
                          biosci.src: scanner

      1.  GERLACHJ@Q Re: Hand Scanner and Autorads.
      2.  GERLACHJ@Q Re: Hand Scanner and Autorads.
      3.  BACKD@QUCD Re: Re: Hand Scanner and Autorads.
      4.  BACKD@QUCD Re: Re: Hand Scanner and Autorads.
      5.  marder@agr Re: Recording scanner.
      6.  GERLACHJ@Q Re: Software for Densitometry from Scanner Images.
      7.  smith@phyl Re: Re: Hand Scanner and Autorads.
      8.  Frank Yue Re: Re: Hand Scanner and Autorads.
      9.  NXK104@psu Re: OCR Software & Scanner.
      10. GERLACHJ@Q Re: Software for Densitometry from Scanner Images.
      11. smith@phyl Re: Re: Hand Scanner and Autorads.
      12. BACKD@QUCD Re: Re: Hand Scanner and Autorads.
 -->  13. djt2@po.CW Re: Scanners for autorads- responses.
      14. extim@lure Re: Scanners for DNA gel densitometry analysis.
      15. david@ASTR Re: to be posted.
      16. morrow@mur Re: REA patterns.
      17. broe@aardv Re: Re: Macintosh Sequence Aligner/Editor?.
      18. BDODSON%VU Re: RE: IMAGE ANALYSIS OF BLOTS AND CAT ASSAYS.

Press ? for Help, q to Quit, u to go up a menu                        Page: 1/3
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

I have used the mail option from within gopher and I have posted you the 
best bits. I hope you find them useful.

Rob "at your service" Harper
--
 ~ 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: bwilliam@oyster.smcm.edu (Bill Williams)
Newsgroups: bionet.software
Subject: Re: InPlot for Mac?
Date: 13 Nov 92 20:55:10 GMT
Organization: St. Mary's College of Maryland
X-UserAgent: Nuntius v1.1.1d10
X-XXMessage-ID: <A7298F64680101D2@williams.smcm.edu>
X-XXDate: Fri, 13 Nov 92 21:59:16 GMT

In article <1992Nov10.000502.20308@reed.edu> Eric Bowman,
bowman@reed.edu writes:
>Does such a product exist for Macintosh?

I use IGOR, and I recommend it with the qualification that it is not
overly user-friendly. It is extremely capable and fast.  It will do all
the things you request:  curve fitting to a myriad of possible
functions (polynomial, Fourier, exponential, etc., etc.), it'll happily
do error bars (it'll calculate them for you, but I find it easier to do
the calculations in Excel), bar plots, scatter plots, you name it.
 
 IGOR is available from WvaeMetrics, PO Box 2088, Lake Osego, OR 97035.
 503-620-3001.  They are reachable at WaveMetrics@AppleLink.Apple.com
___________________________________
William E. Williams, bwilliam@oyster.smcm.edu
Divison of Natural Sciences and Mathematics
St. Mary's College of Maryland
St. Mary's City, MD 20686
Newsgroups: bionet.software
From: francis@monod.Biol.McGill.CA (Francis Ouellette)
Subject: Re: The program Amplify for PCR design - where can I find it???
Organization: McGill University
Date: Wed, 11 Nov 1992 12:21:02 GMT

Bo.Servenius@wblab.lu.se (Bo Servenius) writes:

>Have heard about a program Amplify for designing of PCR primers.
>Is it a freeware/shareware and if so where can I find it for FTP???


Dear Bosse,


from last week on bionet.molbio.methds-reagnts:

---------8<---cut here ----8<-----------------------


*******************************************************************
*                                                                 *
*                Frequently Asked Question (FAQ) list             *
*                for bionet.molbio.methds-reagnts                 *
*                                                                 *
*                Last update was on 01 November 1992              *
*                                                                 *
*******************************************************************
 
 
This FAQ list is available by anonymous ftp to ncifcrf.gov
Simply get the file pub/methods/FAQlist
 
[ lots of usefull stuff removed ]
 
Paul N. Hengen
National Cancer Institute
Frederick Cancer Research and Development Center
Frederick, Maryland 21702-1201 USA
 
e-mail: pnh@ncifcrf.gov
 

[ lots of usefull stuff removed ]


[ from the oligo/primer/pcr section ... ]

***********************
4. Amplify - MAC only
***********************

This software is for use in designing, analyzing, and simulating
experiments involving the polymerase chain reaction (PCR).  PCR is a
technique used by molecular biologists to amplify highly selected
segments of DNA.
 
You can obtain a copy of Amplify from
sumex-aim.stanford.edu via anonymous ftp. Look for the file:
 
      /info-mac/app/amplify-10.hqx
 
The author, Bill Engels, can be reached at WREngels@wisc.macc.edu


 
---------8<---cut here ----8<-----------------------

 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: agnew@gems.vcu.edu
Newsgroups: bionet.software
Subject: Need help on analyzing ECG's
Date: 5 Nov 92 19:01:07 GMT
Organization: Medical College of Virginia

Dear netpeople,
  I'm in search of software and or source code to analyze human ECG/EKG
heart traces...  Please reply to this net address.  Many Thanks!!!
Any leads at all will be much appreciated.

Jim


         /^^^\   \ /   Jim Agnew         | AGNEW@RUBY.VCU.EDU  (Internet)
        /      >  ||   Neurosurgery,     | AGNEW@VCUVAX        (Bitnet)
   /\_/     '   \  /   MCV-VCU           | This disc will self destruct in
 /________________>    Richmond, VA, USA | five seconds.  Good luck, Jim..."
Newsgroups: bionet.software
From: Jens.Burkert@arbi.informatik.uni-oldenburg.de (Jens Burkert)
Subject: wanted: neural spike trains
Organization: University of Oldenburg, Germany
Date: Mon, 9 Nov 1992 13:35:36 GMT
Summary: wanted neural spike trains
Keywords: neural spike

Hello!

I'm looking for spike train data produced from real neurons.

It is for the analyse of stochastic point processe described by Perkel,
Gerstein and Moor (1967) and crosscorrellation analyse.

Spike trains from two interacting (inhibitory or excitatory)
pacemaker (or other) neurons would be very welcome.

The organisation of the data should be in Intervals
e.g.
|   |   |    |   |        <-  neuronal spike train
 10  10  15   10      ms
or 
|   |   |    |   |
0   10  20   35  45  ms

also floating point.

Thank you
Jens Burkert


-- 
Jens Burkert (jens)     *    Abteilung Prozessinformatik
Universitaet Oldenburg   *   DW-2900 Oldenburg  (FRG)
EARN:  Jens.Burkert%arbi.informatik.uni-oldenburg.de@DOLUNI1
ISO:  Jens.Burkert@arbi.informatik.uni-oldenburg.de
From: mangalam@SALK-SC2.SDSC.EDU
Newsgroups: bionet.software
Subject: Mac Primer executable
Date: 12 Nov 92 19:02:04 GMT
Distribution: bionet

Hi,
   Since the Primer gang has still not put the Mac exe up on their FTP
server, and I've received a couple of requests for it, I've bundled the
distribution, with a ThinkC project, and the executable as a binhexed,
self-extracting archive and put it up on our server (salk-sc2.sdsc.edu) in:
[anonymous.mac] (it's a VAX).  Feel free to distribute it, but only as a
complete set (to adhere to the original distribution policy).
   Beware, macaholics, it is the same text-window interface that pops up on
a VAX or PC, but it is certainly handy if you need it.
   The ThinkC project comes to you by the good graces of Richard Cooke of
Universite de Perpignan (COOKE@FRPERP51.bitnet).


   For your info:

Primer benchmarks

                                Sample.seq   Sample2.seq     Sample3.seq   
 
 
SGI Crimson
R4000/4010:50MHz                      6s        instantly          25s     
       
16kB(1')/1MB(2') Cache, 64 MB Main
Standard MIPS compiler

PC Clone
386DX/387:25MHz
64 kB Cache, 8MB Main                 30s           1s             75s
(but only 640kB accessible)
MS QuickC for Windows -> DOS exe

MacIIci
68030/68881:25MHz                     42s           3s             183s
Std Cache card, 8MB Main
Think C 5.0

Cheers
Harry
 

Harry Mangalam                                   Vox:(619) 453-4100, x250
Dept of Biocomputing                                   Fax:(619) 552-1546
The Salk Institute                             mangalam@salk-sc2.sdsc.edu
10010 N Torrey Pines Rd                        mangalam@salk-sgi.sdsc.edu
La Jolla CA 92037                                    mangalam@salk.bitnet

Newsgroups: bionet.software
From: bowman@reed.edu (Eric Bowman (bobo))
Subject: InPlot for Mac?
Organization: Reed College, Portland, OR
Date: Tue, 10 Nov 1992 00:05:02 GMT

My apologies if you see this twice, we're having news problems...

We got an add for some PC software, InPlot, which looks like exactly what
we want for Macs.  Specifically, very general data plotting capabilities
(scatter, line, bar, error bars, etc.), plus non-linear regression, plus
Scatchard plots.

Does such a product exist for Macintosh?

Thanks,
Eric Bowman
bowman@reed.edu