HDTenEightyP/NetNews huggingface dataset:
From: harper@nic.funet.fi (Rob Harper)
Subject: Mailfasta NCBISHELLS GRAILSHELLS
Summary: fasta blast grail blocks
Keywords: E-mail servers
Organization: Finnish University and Research Network (FUNET)
Date: Mon, 7 Sep 92 10:11:35 GMT

I just "approved" an new mailfasta v3.0 for UNIX and NCBI and GRAIL
shells for VMS. They have been posted to bionet.software.sources
as share files. The original posters were Thon De Boer and Foteos Macrides

Since the E-mail server at genbank.bio.net will soon disappear over
the blue event horizon it is good that these new scripts are now
available since it will ensure continuity of service. Nice work.

I am particularly impressed by mailfasta since it allows 
fasta, blast, blocks, grail, searches, which means that it
is pointing at different server sites on the internet.
Fasta for example is pointing to Japan.

RGDS -=ROB=-
From: kleinschmidt@mcclb0.med.nyu.edu
Newsgroups: bionet.software
Subject: How to get PAUP
Date: 7 Sep 92 19:01:51 GMT
Organization: NYU Medical Center, New York, NY 10016, USA

How to get PAUP (Phylogenetic Analysis Using Parsimony):

The only up-to-date version of PAUP presently available is version 3.0s for 
the Mac (dated Dec. 1991).  I understand that David Swofford is also 
working on an updated version for PC-DOS machines (under Windows?) as well 
as on a universal graphical interface which will first be implemented in a 
Unix version.

Version 3.0s of PAUP for the Mac can be obtained from:

David L. Swofford
c/o Mary Lou Williamson
Illinois Natural History Survey
607 E. Peabody Drive
Champaign, ILL 61820, USA
Phone: 217-333-6846

Send to Mary Lou Williamson at the address above: (1) a check for $50.00 
($60 outside North America) drawn on a U.S. bank and made out to the 
University of Illinois/IHNS, or an International Money Order, (2) a note 
stating that you understand that the present version of the User's Manual 
is a draft that is incomplete in many parts, and that this is acceptable to 
you.  You will receive the program with manual within 2-3 weeks.  A final 
version of the manual will be sent to you once it is finished.

PAUP is an excellent program that is quite usable even with the present 
incomplete manual.  It runs even on classic Macs.  For $50, it is a 
bargain.  If you're in the habit of ripping off software companies by using 
illegal copies of their products, DON'T do this with PAUP!  David Swofford 
provides a tremendous service to molecular phylogenists with this program, 
and the amount he charges goes into a Univ. of Ill. account and is used 
only to cover costs and pay for some upgrades in hardware and software that 
make his life as a program developer easier.  You wouldn't want the man to 
get disgruntled and stop improving his program, an activity to which he 
devotes a good amount of his time (undoubtedly too much, from his 
perspective).  The PAUP production is a one-man operation, and the reason 
why it is somewhat inconvenient to obtain the program is simply because 
David's use of a simple "cash sales" account keeps the price of the program 
to a minimum.  Overseas users are probably best off sending in an 
International Money Order.

I have been using public domain (or minimal cost) software for multiple 
sequence alignment and phylogeny reconstruction for the past 6 months, and 
this is a good occasion for me to express my gratitude to all those who put 
out a great deal of effort to make this software available to the rest of 
us.  My thanks specifically go to Joe Felsenstein (Phylip), David Swofford 
(PAUP), Jotun Hein (Treealign), Don Gilbert (Readseq), Steve Clark 
(Maligned), Des Higgins (ClustalV), and to the administrators of various 
Internet-accessible ftp archives, in particular Don Gilbert 
(ftp.bio.indiana.edu) and Dan Davison (ftp.bchs.uh.edu).

Jochen Kleinschmidt
NYU Medical Center
Organization: University of Maine System
Date: Saturday, 12 Sep 1992 10:56:02 EDT
From: Robert Roxby <RROXBY@MAINE.MAINE.EDU>
Newsgroups: bionet.software
Subject: Where ClustalV in .ZIP format?

I am having a struggle getting a working copy of ClustalV
from EMBL, I guess because I am too dumb to master the
decompression regimen.  Does anybody know where it can be
found in the .ZIP format?  Thank you.
-Bob.
Newsgroups: bionet.software
From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert)
Subject: Internet crackers and security advice
Organization: Biology, Indiana University - Bloomington
Date: Mon, 7 Sep 1992 03:04:26 GMT


Over the course of three weeks in August, two Sun computers that I
manage, including the IUBio archive host, were broken into by an
Internet cracker.  This person, or persons, apparently used known
security holes in the standard SunOS Unix software to gain access
via NFS, logins and full superuser privileges.  This cracker then 
altered important system binaries to hide his/her activities, to gain
future access and possibly just to cause me hassles.  It took me
about a week of work and finally erasing and reinstalling the / and /usr
Unix partitions to clean out the damage on ftp.bio.indiana.edu.  I
think the archive host is now working properly for ftp and gopher
access.

Prior to this, I had not paid much attention to security concerns
for Internet-accessible computers.  I thought passwords were enough,
and there wasn't anything of interest to crackers on my computers.
My mistake.  Among other things, the cracker used one of my hosts
to break into other computers, and tried to gain control of a modem
and telephone to dial out to other computers.  At one point, this
cracker had broken in at several computers in USA, Australia
and possibly Norway, and was shuffling files among them as if s/he
owned them all.

To the best of my knowledge, the anonymous ftp and internet gopher
server software on ftp.bio.indiana.edu were not used by the
cracker in gaining access, but known security holes in SunOS 4.1.1
were used.

The best advice I got in dealing with these activities was from
the Computer Emergency Response Team (CERT).  They keep tabs on
foul and criminal activities like I was experiencing.  In Febuary
and June, they posted advisories about Internet breakins such as
this one.  They also keep an archive of advisories on known security
holes and ways to patch them.  I read these, installed security 
patches that apply to my systems, and am now running a security
checking program (COPS) available from CERT.  

For those of you who manage Unix or VMS systems, I strongly
recommend that you read thru the CERT advisories that apply to
your systems, including their general advisories on Internet
intruders, if you haven't done so recently.   If you have an 
Internet-connected computer, the only way to insure it isn't
broken into by bad people is to be vigilant on security.

Anonymous ftp to cert.org ((192.88.209.5), 
  get /pub/cert_advisories/01-README.
Internet E-mail: cert@cert.org


-- Don

-- 
Don Gilbert                                     gilbert@bio.indiana.edu
biocomputing office, biology dept., indiana univ., bloomington, in 47405
Newsgroups: bionet.software
From: ecec@quads.uchicago.edu (Eric Cabot)
Subject: Re: Sequence Editor wanted
Reply-To: ecec@midway.uchicago.edu
Organization: University of Chicago Computing Organizations
Date: Tue, 8 Sep 1992 17:43:00 GMT

In article <t4phage.715623093@milton> t4phage@milton.u.washington.edu (Betty Kutter) writes:
>
>For the work I have been doing on the bacteriophage T4 genome
>I have found that an editor for sequence work would be useful.
>I have setup an example at the bottom of this message and
>I will explain the various parts.  I would like a work space of unlimited
>(something wider than 10K bases) width and 25 to 40 lines in
>length.  The work space would be divided into two major areas

[stuff deleted]

>reply to t4phage@u.washington.edu
>
I recommend you obtain the file esee109e.zip from the anonymous
ftp site at ftp.bio.indiana.edu. It is in the directory molbio/ibmpc
and it is a binary file. Send me email if you need help/instructions
on using anonymous ftp.   

Regards,

Eric Cabot,
University of Chicago 


-- 
=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=v=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=
    Eric Cabot                         |       "Non Nobis Nati Solum" 
ecec@midway.uchicago.edu               | 
=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=v=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=
From: camkowal@ubvmsd.cc.buffalo.edu (David Kowalski)
Newsgroups: bionet.software
Subject: Software for colony counting
Date: 11 Sep 92 00:58:00 GMT
Organization: University at Buffalo
News-Software: VAX/VMS VNEWS 1.41


      	Can anyone out there direct me to DOS software
that is capable of counting colonies on plates by analysis
of a scanned image (eg. TIFF files or other HP Scanjet
files) of the plates?
From: OCONNOR@GEODE.BIOTECH.CDC.GOV
Newsgroups: bionet.software
Subject: Tree Drawing Programs
Date: 5 Sep 92 18:24:03 GMT
Distribution: bionet

Hello:

I am using the PHYLIP package (v3.4) from J. Felsenstein.  Can anyone
point me to a program which will accept a PHYLIP treefile as input and
plot the tree to a HP laserjet?  The DRAWTREE and DRAWGRAM programs
included with PHYLIP work well, but I would like to find something
which will allow me a bit more control over the appearance of the
plot.

Thanks.

Steve                                 oconnor@geode.biotech.cdc.gov

Steve O'Connor
Division of Bacterial and Mycotic Diseases
National Center for Infectious Diseases
CDC
Fri, 11 Sep 1992 19: 57:54 +0100
               Fri, 11 Sep 1992 15: 28:10 +0100
               Fri, 11 Sep 1992 18: 26:40 +0100
From: gartmann@VMS.MPIIB-FREIBURG.MPG.dbp.de (Christoph Gartmann)
Newsgroups: bionet.software
Subject: RE: SRS 2.1 available via anon ftp
Date: 11 Sep 92 17:26:40 GMT
Distribution: bionet
Content-Identifier: 12
Original-To: bio-software@uk.ac.daresbury
Conversion: Prohibited

Just a small appendix to the SRS announcement from Rodrigo:
   Currently SRS requires the VAX-VMS operating system. Although it is written
   in C, it is not possible to compile it under any other operating system.

+-------------------------------------------------------------------------+
| Christoph Gartmann          Phone : +49-761-5108-465   Fax: -221        |
| Max-Planck-Institut fuer    PSI   : PSI%026245761030173::GARTMANN       |
| Immunbiologie               X400  : S=gartmann;OU=vms;O=mpiib-freiburg; |
| Stuebeweg 51                        P=mpg;A=dbp;C=de                    |
| D-7800  Freiburg            RFC   : gartmann%vms.mpiib-freiburg.mpg.dbp.|
| FRG                                 de@relay.cs.net                     |
+-------------------------------------------------------------------------+
Newsgroups: bionet.software
From: frist@ccu.umanitoba.ca ()
Subject: Re: Internet crackers and security advice
Organization: University of Manitoba, Winnipeg, Manitoba, Canada
Distribution: bionet
Date: Thu, 10 Sep 1992 17:46:23 GMT

In article <zxmkr08.716131405@mailserv> zxmkr08@mailserv.zdv.uni-tuebingen.de (Cornelius Krasel) writes:
>I have seen a password cracking program in action. Unfortunately it
>does not help to simply include digits or punctuation into "real words",
>since at least this program was prepared for it and cracked things like
>z1ebra without any problems. As far as I remember, the program used
>several approaches: first, it tried all usernames available on this 
>particular computer; second, it tested an internal (editable) word
>list; third, it checked changes in spelling, such as mixed upper-
>or lowercase, or interspersed digits. It was fairly successful...

Perhaps I'm displaying my ignorance of operating systems here, but 
shouldn't it be fairly easy for the system to detect a cracking program?
By definition, the process of trying to login thousands of times with
a long series of possible passwords, as described above, should be
easily distinguishable from the user who fumbles his password and finally
logs in on the 5th try. I would think such a tally of unsuccessful 
login attempts could automatically trigger a message to be sent to
the system operator at, say, the 20th failure. Shouldn't such an easy
fix be built in to any operating system?  Maybe I'm oversimplifying
the situation.
>
>--Cornelius (by no means an expert of computer security).
>--
>/* 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)                  */

===============================================================================
Brian Fristensky                | Unintentionally funny qoute of the month:
Department of Plant Science     | 
University of Manitoba          | Rev. Jerry Falwell denounces Bill Clinton,
Winnipeg, MB R3T 2N2  CANADA    | saying that his "misquoting and manipulating
frist@ccu.umanitoba.ca          | holy scripture for political purposes should 
Office phone:   204-474-6085    | be offensive to millions of Americans." 
FAX:            204-261-5732    |
===============================================================================
From: kleinschmidt@mcclb0.med.nyu.edu
Newsgroups: bionet.software
Subject: Re: Calculating free Ca2++ with EGTA buffers
Date: 11 Sep 92 03:56:01 GMT
Organization: NYU Medical Center, New York, NY 10016, USA

Sorry about the formatting of the preceding message.  Here is the 
clean copy:
 
Three years ago, I wrote a program named CABUFFER that allows you to 
calculate the free concentrations of all ionic species in a mixture of 
up to four divalent ions (e.g. Mg, Ca, Sr, Ba) and up to four 
different divalent ion buffers (e.g. EGTA, EDTA, NTA, HEDTA, citrate 
etc.).  Free parameters are temperature, pH and ionic strength.  The 
program was written in structured Basic and compiled with Borland's 
Turbo Basic v. 1.0 or with Microsoft's Quickbasic v 4.0 under MS-DOS.  
It runs very fast on PC's outfitted with a math coprocessor.  A 
slightly less capable program, CABUF, that runs reasonably fast even 
on machines without math coprocessor is also available.  At that time, 
and perhaps still now, CABUFFER probably was one of the best and most 
flexible programs of that sort available in the public domain.
 
This program has been passed around and is presently being used by a 
number of labs, apparently with good results.  I can make it available 
to anyone who cares for it.  Way back, I actually meant to write a 
paper on the use of Ca-buffers in physiology and on the traps one can 
fall into doing that.  Alas, the manuscript was never completed but 
early drafts of various sections are on the diskette.  They may make 
tedious but instructive reading for those who care to understand what 
they are doing when they make up and use Ca-buffers.  Unfortunately, 
all the equations are missing from the electronic version; I couldn't 
get them into ASCII format.
 
All the files take up about 280 Kb of space, including an introductory 
readme file.  The CABUFFER exe file is about 80 Kb long.  The Basic 
source code is also provided, so that you can modify it and recompile 
it with Turbo Basic or Quickbasic.  I can send all of this out on 
diskette, or better still, see if I can put the files into a public 
directory on our VAX from which you can download them via anonymous 
ftp.  I will have to talk to our system administrator about this.
 
I have little time to support this program.  Also, if you use it, you 
do so at your own risk.  But I believe that its use is easy and 
self-explanatory, and I also think that it is largely bug-free.  In 
absolutely critical applications you should always rely on using 
carefully calibrated Ca-sensitive electrodes (this is a major 
undertaking!).  Short of that, this program may get you somewhere, 
certainly in simple EGTA buffers.
 
Jochen Kleinschmidt
NYU Medical Center
kleinschmidt@mcclb0.med.nyu.edu
 
Newsgroups: bionet.software
From: gchacko@magnus.acs.ohio-state.edu (George W Chacko)
Subject: Reverse Complement
Organization: The Ohio State University
Date: Thu, 10 Sep 1992 16:59:29 GMT

I need to generate the reverse complement of a DNA sequence on a Unix
machine. Transferring the file to a VAx and using GCG is laborious.
I've been playing around with awk and rev rather unsuccessfully. Does
anyone have a script that will do this?

Thanks

George




Newsgroups: bionet.software.sources
From: gilbertd@fly.bio.indiana.edu (Don Gilbert)
Subject: IUBio Archive update
Organization: Biology, Indiana University - Bloomington
Date: Fri, 11 Sep 1992 22:26:01 GMT


This is an update notice of new information available at IUBio archive,
either thru anonymous ftp or using Internet Gopher to ftp.bio.indiana.edu. 

Additions to IUBio Gopher hole include ........................

   Drosophila/
     Drosophila Redbook search <?>
 

New archive files include.........................................
...size...date.....path/name................
   98120 Sep 10 ./biology/ibmpc/winamova.zip   -- pop genetics, mswindows

         Sep 11 ./fly/flybase/..(various)      -- M.Ashburner fly database 
     838 Sep  9 ./fly/mapping.txt 	       -- other fly data updates
  268672 Sep  9 ./fly/flylist.txt 
  119477 Sep  9 ./fly/new_P.txt 
   10342 Sep  9 ./fly/balancers.txt 

   28370 Aug 17 ./molbio/align/cap.tar.Z 	-- contig assembly
   53350 Sep  2 ./molbio/ibmpc/dotplot-2.0.zip  -- dot plot
   29102 Sep  5 ./molbio/unix/mailfasta3.0      -- sequence search by mail
-- 
Don Gilbert                                     gilbert@bio.indiana.edu
biocomputing office, biology dept., indiana univ., bloomington, in 47405
From: danj@WELCHGATE.WELCH.JHU.EDU (Dan Jacobson x-8453)
Newsgroups: bionet.software
Subject: Re: Fly
Date: 8 Sep 92 16:32:22 GMT
Distribution: bionet


The Ip address is as follows:


Name:    fly.bio.indiana.edu
Address:  129.79.224.25


Best of luck,

Dan Jacobson

danj@welchgate.welch.jhu.edu
From: bss2aj@surrey.ac.uk (Alan Jennings)
Newsgroups: bionet.software
Subject: Fly
Date: 8 Sep 92 13:51:35 GMT
Distribution: bionet
Mailer: Elm [revision: 66.25]
Original-To: bio-soft@uk.ac.daresbury (biosoft newsgroup)

Dear Netters,

	This site has only recently been connected to the internet, and,
as yet, has no database or link to one of names for sites. We therefore
have to use the numeric addresses. 

	I would like to obtain the mailfast program mentioned here a
short while ago, but I dont have the numeric address for the fly server
at Indiana. Could someo9ne please e-mail it to me here at:-

		bss2aj@surrey.ac.uk

		Thanks in advance

			Alan
_____________________________________________________________
Alan Jennings                  |  "Time is an illusion.......
University of Surrey, UK.      |   lunchtime doubly so."
e-mail bss2aj@central.surrey.ac.uk
From: THOMSTEVENS@BIOTECHNET.COM
Newsgroups: bionet.software
Subject: review of manuscript for BioTechnit ques
Date: 15 Sep 92 18:23:57 GMT
Distribution: bionet

TO:	ALL
FROM:	Thomas J. Stevens, Assistant Editor, BioTechniques
RE:	Use of a programmable calculator for storing cloning library data
 
If you have used a programmable calculator, preferably the Hewlett-Packard
HP48SX, for storing DNA and peptide sequencing information, I would be
interested in asking you to review a short manuscript for BioTechniques.
 
Thomas J. Stevens, Assistant Editor
BioTechniques
Eaton Publishing
154 East Central Street
Natick, MA 01760 USA
phone (508) 655-8282  fax (508) 655-9910
From: pinelli@uniwa.uwa.edu.au (Mario Pinelli)
Newsgroups: bionet.software
Subject: Re: Reverse Complement
Date: 13 Sep 1992 14:24:45 +0800
Organization: The University of Westrn Australia
NNTP-Posting-Host: uniwa.uwa.edu.au

In <1992Sep10.165929.3773@magnus.acs.ohio-state.edu> gchacko@magnus.acs.ohio-state.edu (George W Chacko) writes:

>I need to generate the reverse complement of a DNA sequence on a Unix
>machine. Transferring the file to a VAx and using GCG is laborious.

Try the following 'one-liner':

tail -r INPUTFILE | rev | tr atgcATGC tacgTACG > OUTPUTFILE

It should do what you ask.  Your input file must contain DNA sequence only,
comment lines beginning with '>' are NOT ignored and will be read as sequence. 
I could probably find a way to handle that if required.


If you want to put this into a script file try:

if test $1                                          
then                                                
        tail -r $1 | rev | tr atgcATGC tacgTACG >$1.rev
else                                                
        echo "usage: $0 <dna_sequence_file>"        
fi

Make the file executable with the command 'chmod 755 script-flie'.  It will
produce an output file with the extension .rev when called from the
command line, e.g.  revcomp humtnfa    ==produces==>  humtnfa.rev
I'm currently working on some other unix scripts for simple sequence 
manipulation based on traditional unix commands.  Does anyone have
any suggestions? ...dare I ask!


Mario Pinelli                  (pinelli@murdoch.edu.au)

Biotechnology Programme,
Murdoch University,
Murdoch, W.A., 6150,
Australia.
From: jasper@vax.path.ox.ac.uk
Newsgroups: bionet.software
Subject: Re: Thanks for info on mac/pc exchange
Date: 4 Sep 92 17:48:47 GMT
Distribution: bionet
Organization: Oxford University Molecular Biology Data Centre
Nntp-Posting-User: jasper



> My thanks to the over two dozen people who replied to my question about
> Mac to PC file exchange.  I'm now trying to learn how to use the
> Apple File Exchange utility that came with the Mac.  (For anyone else

Bill,

	sorry I didn't pick this up before, but an option that no-one else
seems to have mentioned yet is Apple's PC Exchange. Originally billed as part
of System 7 it didn't make it in time and we got our first copies this week
with some new Macs. It is fully system 7 integrated, read/writes/initializes
DOS disks (high density anyway, I haven't tested a low density one, though I
have a drive somewhere if anyone feels they really want to know :)  and you
can configure it to display icons of data files for software where there is a
PC-Mac pair of versions. 

	It cost us 38 pounds sterling, probably costs US$38 therefore, and I 
imagine it will become part of system 7 at some time in the future, though at 
present that is a one copy - one machine license.

	Now this has *got* to better than Apple file exchange !

	So, check out your local Apple dealer!

	I guess it goes without saying - I liked it!

regards,     jasper

Jasper Rees
Oxford University

jasper@vax.path.ox.ac.uk

Usual disclaimers apply (shame really :)
Newsgroups: bionet.software
From: tabq7@isuvax.iastate.edu
Subject: mapmaker
Reply-To: tabq7@isuvax.iastate.edu
Organization: Iowa State University, Ames, Iowa
Date: Tue, 15 Sep 1992 18:38:53 GMT

Could someone please direct me to where I might find the latest version
of mapmaker for Sun Workstations?


Thanks,

Phil
Newsgroups: bionet.software