From owner-www@net.bio.net Sun Jan 01 22:00:00 1995
Newsgroups: bionet.software.www
Path: biosci!newshost.lanl.gov!news.ttu.edu!seas.smu.edu!uunet!cs.utexas.edu!howland.reston.ans.net!pipex!sunic!ugle.unit.no!trane.uninett.no!daresbury!bioftp.unibas.ch!moderate
From: leen@bio-3.bsd.uchicago.edu (Lee Newberg)
Subject: Re: [Q] CGI Scripts [part 2]
Message-ID: <1994Dec31.215012.11408@midway.uchicago.edu>
Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland)
Organization: U of Chicago, Biological Sciences Division
Date: Sat, 31 Dec 1994 21:50:12 GMT
Approved: bio-www@comp.bioz.unibas.ch
Lines: 13

Check out http://hoohoo.ncsa.uiuc.edu/cgi/overview.html for
information on CGI scripts.

)))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))
			  L	   N	   The Office of Academic Computing
			     e	      e	       Biological Sciences Division
				e	 w	  The University of Chicago
					    b	       924 East 57th Street
L-Newberg@uchicago.edu			       e	  Chicago, Illinois
http://http.bsd.uchicago.edu/~l-newberg/	  r		 60637-5415
(312) 702-2056 x5-1604 or Fax (312) 702-2280	     g			USA
)))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))


From owner-www@net.bio.net Sun Jan 01 22:00:00 1995
Newsgroups: bionet.software.www
Path: biosci!newshost.lanl.gov!news.ttu.edu!seas.smu.edu!uunet!pipex!sunic!trane.uninett.no!daresbury!bioftp.unibas.ch!moderate
From: micha@amber.biophys.uni-duesseldorf.de ()
Subject: Re: [Q] CGI Scripts [part 1]
Message-ID: <3e4g5e$f6g@news.rz.uni-duesseldorf.de>
Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland)
Organization: Biophysics Dept., Univ. Duesseldorf
Date: Sat, 31 Dec 1994 20:49:36 GMT
Approved: bio-www@comp.bioz.unibas.ch
Lines: 51

Jeff Matthews (mookie@physics.ubc.ca) wrote:
: I'm trying to get a Web site set up for Radiobiology and I'm trying to
: work out support for forms. I want to take the form output and append
: it into a html file that can be accessed. However, I know almost 
: nothing about how to write these scripts? 
: Can anyone help?

Jeff,
together with (at least the CERN) httpd there should be a program 
called 'cgiparse'. This program should help you extracting the data
either from the command line fed into the script, or from the environment
variables (keys) that are set by httpd upon calling the script. (I think since
the GCI-release the keys are the method of choice for you) 
The method of passing the forms data via separate keys is described in the
server's documentation; this documentation is available online at CERN, for
that one.
If you want only to append form output to a file, 'cgiparse -keywords > file'
should do the job.  (Unix scripts, VMS is a bit more tricky ...)
If you want to give some feedback to the user submitting the form, you need to
write the HTML text to stdout (using echo, I think), like

Content-type: text/html

<html>
<head>
<title>Form Feedback</title>
</head>
<body>
<h2>Your form input has been processed, good bye!</h2>
You can check the result <A HREF="/where/ever/you/like/file">here</A>!
</body>
</html>

(the empty line between the Content-type line and <html> is IMPORTANT!)

The URL to CERN's manual is 
<A HREF="http://www11.w3.org/Hypertext/WWW/Daemon/User/Guide.html">this</A>!

The section about CGI/1.1 explains it all, and if all else fails, run the
server in debug mode from a terminal :-(
 
: Thanks

: J.B. Matthews
: Medical Biophysics Dept.
: BC Cancer Research Centre
: mookie@physics.ubc.ca

Michael Schmitz
Biophysics, Uni-Duesseldorf


From owner-www@net.bio.net Thu Jan 05 22:00:00 1995
Newsgroups: bionet.software.www
Path: biosci!CS.Arizona.EDU!uunet!sunic!trane.uninett.no!daresbury!bioftp.unibas.ch!moderate
From: eggenber (Florian Eggenberger)
Subject: WWW Introduction: Part 17
Message-ID: <1995Jan4.151721.4587@comp.bioz.unibas.ch>
Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland)
Organization: EMBnet Switzerland [Basel]
Date: Wed, 4 Jan 1995 15:17:21 GMT
Approved: bio-www@comp.bioz.unibas.ch
Lines: 93


WWW INTRODUCTION        January 1995
================

PART 17: Customizing WWW
------------------------

This is the seventeenth part of a series of postings describing the concept 
of the World-Wide Web and guiding anyone who is interested in obtaining and 
setting up the software required to access the Web.

WWW browsers come with an address of a document to start with, a so-called 
Home Page. Usually, this document does not include pointers to the WWW 
sites you are interested in. Accessing information by following the 
hyperlinks provided may therefore take some time. A quicker and more 
convenient route to the World-Wide Web is to use your own Home Page, a WWW 
starting point tailor-made for your special needs. This will speed up data 
access as the browser then starts with a local file instead of going out on 
the network and lets you work much more efficiently since you can include 
pointers to your favorite WWW sites.

Like any WWW document, Home Pages are written in HTML. See the previous 
part of this introduction if you don't know what HTML is. The language 
elements described therein are sufficient for a simple HTML document. So, 
go ahead and create your own Home Page. Specify the title and heading of 
the document and include a list of hyperlinks to sites that provide the 
information you want to access often. (Some links that might be of interest 
for biologists have been provided in part 15 of this series of postings.) 
Save your document as "text only", then open it with your WWW browser and 
re-edit the source, if required. How to start WWW with your own Home Page 
depends on the browser software and operation system installed on your 
machine. The following descriptions apply to some of those browsers for 
which installation has been described in previous parts of this 
introduction:

*Lynx and NCSA Mosaic for X
On UNIX use the shell variable WWW_HOME to specify the URL of your Home 
Page. Add a line to the appropriate start-up file: 
  when running ksh:  export WWW_HOME=URL
  when running csh:  setenv WWW_HOME URL
On VMS use the logical name WWW_HOME to specify the URL of your Home Page. 
Add a line to the startup file or to the command file that invokes WWW:
  $ define "WWW_HOME" "URL"

*MacWeb
Start MacWeb. Select "Preferences..." from the "File" menu. Replace the URL 
of the default Home Page by the URL of your Home Page.
 
*NCSA Mosaic for the Macintosh
Start Mosaic. Select "Preferences..." from the "Options" menu. Then select 
"Misc" and replace the URL of the default Home Page by the URL of your Home 
Page.

*NCSA Mosaic for Windows
Quit Mosaic. Open the file "mosaic.ini" in the Windows directory. Replace 
the URL of the default Home Page by the URL of your Home Page.

*WinWeb
Quit WinWeb. Open the file "winweb.ini" in the Windows directory. Replace 
the URL of the default Home Page by the URL of your Home Page.

The WWW browser can handle only a restricted range of file types, but those 
files that cannot be handled internally are processed by so-called external 
viewers. The mapping of MIME types and file extensions to external viewers 
is configurable. MS-Windows browsers let you specify MIME types and file 
extensions in the appropriate "*.ini" file in the Windows directory. Using 
Lynx, the settings can be configured in the file "lynx.cfg" . MacWeb users 
can configure their browser by selecting the "Helpers..." and "Suffixes..." 
options in the "Edit" menu.

Most WWW browser provide various other parameters that can be configured. 
To change the default settings of these parameters:

* Lynx: type "o"
* MacWeb: select "Preferences" in the "File" menu.
* MacMosaic: select "Preferences..." in the "Options" menu.
* MS-Windows browsers: edit the "*.ini" file in the Windows directory.
* Mosaic for X: select the "Options" menu.

Go ahead and make changes according to your preferences.


Florian Eggenberger
EMBnet Switzerland

-- 
+------------------------------+--------------------------------+
|  F. Eggenberger, Ph.D.       |  eggenber@comp.bioz.unibas.ch  |
|  Biocomputing                |  eggenberger1@ubaclu.unibas.ch |        
|  University of Basel         |  Fax  +41 / 61 267 20 78       | 
|  Switzerland                 |  Tel  +41 / 61 267 22 47       | 
+------------------------------+--------------------------------+


From owner-www@net.bio.net Mon Jan 09 22:00:00 1995
Newsgroups: bionet.software.www
Path: biosci!daresbury!bioftp.unibas.ch!moderate
From: eggenber (Florian Eggenberger)
Subject: Re: WWW Introduction: Part 17
Message-ID: <1995Jan10.133526.29574@comp.bioz.unibas.ch>
Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland)
Organization: EMBnet Switzerland [Basel]
Date: Tue, 10 Jan 1995 13:35:26 GMT
Approved: bio-www@comp.bioz.unibas.ch
Lines: 37

In article <1995Jan9.211927.10436@nomina.lu.se>, Bo Servenius <bo.servenius@wblab.lu.se> writes:
|> 
|> In article <1995Jan4.151721.4587@comp.bioz.unibas.ch> eggenber,  writes:
|> >WWW INTRODUCTION        January 1995
|> >================
|> >
|> >PART 17: Customizing WWW
|> >------------------------
|> 
|> Please supply the url to the page containing this info at the top of all
|> your news.

This posting is part of a series of articles that have been posted to
bionet.software.www. Previous articles are also available via ftp and http:
nic.switch.ch/mirror/embnet-ch/archive_data/***_version.txt
http://www.ch.embnet.org/bio-www/teaching.html

|> BTW you did not mention Netscape in your posting. Hope you have started

Sure, there are a lot of other software products available including:
Booklink, SpryMosaic, Cello, SlipKnot, AMosaic, Emacs-W3, OmniWeb, MidasWWW,
Viola, Chimera, CERN's line-browser etc. The aim of this series, however, was 
not to provide a thorough survey of browsers available but rather to answer
the very basic questions as what is the World-Wide Web, what is available
on the Web and how to get and install the software required to access the Web.


Florian Eggenberger

-- 
+------------------------------+--------------------------------+
|  F. Eggenberger, Ph.D.       |  eggenber@comp.bioz.unibas.ch  |
|  Biocomputing                |  eggenberger1@ubaclu.unibas.ch |        
|  University of Basel         |  Fax  +41 / 61 267 20 78       | 
|  Switzerland                 |  Tel  +41 / 61 267 22 47       | 
+------------------------------+--------------------------------+


From owner-www@net.bio.net Mon Jan 09 22:00:00 1995
Newsgroups: bionet.software.www
Path: biosci!daresbury!bioftp.unibas.ch!moderate
From: Bo Servenius <bo.servenius@wblab.lu.se>
Subject: Re: WWW Introduction: Part 17
Message-ID: <1995Jan9.211927.10436@nomina.lu.se>
Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland)
Organization: EMBnet Switzerland [Basel]
Date: Mon, 9 Jan 1995 21:19:32 GMT
Approved: bio-www@comp.bioz.unibas.ch
Lines: 44

Newsgroups: bionet.software.www
Path: bosse-q840.wblab.lu.se!bo.servenius
Content-Type: text/plain; charset=ISO-8859-1
X-Xxmessage-Id: <AB37668C7A023821@bosse-q840.wblab.lu.se>
X-Xxdate: Mon, 9 Jan 1995 21:17:48 GMT
Sender: news@nomina.lu.se (USENET News System)
Nntp-Posting-Host: bosse-q840.wblab.lu.se
Content-Transfer-Encoding: 8bit
Organization: lund university
X-Newsreader: Nuntius Version 1.3b18_68K
References: <1995Jan4.151721.4587@comp.bioz.unibas.ch>
Mime-Version: 1.0
Date: Mon, 9 Jan 1995 21:19:27 GMT

In article <1995Jan4.151721.4587@comp.bioz.unibas.ch> eggenber,  writes:
>WWW INTRODUCTION        January 1995
>================
>
>PART 17: Customizing WWW
>------------------------

Please supply the url to the page containing this info at the top of all
your news.
I think that should help many of us veru much.

BTW you did not mention Netscape in your posting. Hope you have started
to use this superb client. Much better than any I have seen to date.

yours

bosse
_______________________________________________________________________
______
Bo Servenius, Ph.D                      |       bo.servenius@wblab.lu.se
The Wallenberg lab                      |       http://www.wblab.lu.se
Lund University                         |       phone:  +46-46-104325
office
P.O.Box 7031                            |               +46-46-104640 lab 
S-220 07 Lund                           |               +46-46-159194 home
Sweden                                  |       fax     +46-46-104324
Europe                                  |       pager:  +46-0740-153870
________________________________________|______________________________
______


From owner-www@net.bio.net Sun Jan 15 22:00:00 1995
Newsgroups: bionet.software.www
Path: biosci!daresbury!bioftp.unibas.ch!moderate
From: Frank Norman <f-norman@nimr.mrc.ac.uk>
Subject: Medical Research Council (UK) WWW Home Page
Message-ID: <3fbfk7$le2@mercury.hgmp.mrc.ac.uk>
Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland)
Organization: MRC Human Genome Resource Centre
Date: Sun, 15 Jan 1995 15:39:51 GMT
Approved: bio-www@comp.bioz.unibas.ch
Lines: 22

A Medical Research Council WWW Home Page is now available:

<a href="http://www.nimr.mrc.ac.uk/MRC">Medical Research Council (UK) </a>

The Medical Research Council (MRC) promotes the balanced development 
of medical and related biological research in the UK. The Council receives 
an annual Grant in aid from Parliament via the Office of Science and 
Technology. It also receives funds for or works with a number of 
government departments, industry and charities. It has close links 
with the Health Departments and the other Research Councils. 
   
The Home Page includes information about MRC Institutes and Units, 
Interdisciplinary Research Centres, and about other UK Research 
Councils.  Hyperlinks are provided where available.  

Frank Norman
Deputy Librarian
National Institute for Medical Research
The Ridgeway
Mill Hill
London NW7 1AA


From owner-www@net.bio.net Sun Jan 15 22:00:00 1995
Newsgroups: bionet.software.www
Path: biosci!daresbury!bioftp.unibas.ch!moderate
From: robison@golgi.harvard.edu (Keith Robison)
Subject: Announce: The 100Kb Club
Message-ID: <CMM-RU.1.4.790042453.biohelp@net.bio.net>
Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland)
Organization: Harvard University, Cambridge, Massachusetts
Date: Fri, 13 Jan 1995 05:10:01 GMT
Approved: bio-www@comp.bioz.unibas.ch
Lines: 18


	Since it is a subject that pops up frequently, I have 
created an HTML listing of all publically-available DNA sequences 
100Kb or longer. It is available at the URL

	http://golgi.harvard.edu/100kb/

Please let me know of any corrections or updates to this list.  
In particular, I don't always hear immediately about new big contigs in
the Saccharomyces or Caenorhabditis genomes.

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

robison@mito.harvard.edu 


From owner-www@net.bio.net Mon Jan 16 22:00:00 1995
Newsgroups: bionet.software.www
Path: biosci!daresbury!bioftp.unibas.ch!moderate
From: David Featherstone
Subject: GDB & OMIM Training via WWW
Message-ID: <1995Jan16.183912.28199@comp.bioz.unibas.ch>
Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland)
Organization: EMBnet Switzerland [Basel]
Date: Mon, 16 Jan 1995 18:39:12 GMT
Approved: bio-www@comp.bioz.unibas.ch
Lines: 62

[ Article crossposted from bionet.molbio.gdb ]
[ Posted on Mon, 16 Jan 1995 12:16:53 GMT ]

                    GDB & OMIM On-line Training
                              via the
                           World Wide Web

Dear Users of GDB and OMIM;

	We are pleased to announce our on-line training course for
GDB & OMIM.  If you have a WWW browser on your workstation, PC or
Macintosh, simply point it to:

	http://www.caos.kun.nl/genomics/GDB_OMIM_TOC.html

and begin!

	The course can be taken in two modes: interactively, with
a parallel GDB or OMIM session, so you may try the commands as they
are described, or passively, reading and looking at the results shown
in the screen "snap-shots" included on the pages. I recommend the
interactive mode.

	Users attempting the entire course, trying the examples and
checking the results, should set aside about six hours. Further, I
suggest using three hours on each of two days.

	This course is continually updated. I try to make certain
the answers to the example questions are current with the databases,
but with daily updates to the databases, you might notice some
differences between my answers and yours. Please TELL ME when you
find a discrepancy, and I'll correct it!

	Finally, please note that I have tried to take full advantage
of the graphics capabilities of most WWW servers; if you find yourself
on a S L O W connection to our facility, and the pages take
inconveniently long to load, try turning OFF the "automatic image
loading" feature of your WWW client. For example, in the Options
menu of NCSA Mosaic, select
	"Delay Image Loading".
In Mosaic Netscape, go to the Options menu and de-select
	"Auto Load Images".
Those of you using Lynx, the text-only WWW browsing tool, will miss
the graphics, of course, but can compensate by printing the pages
and using them to guide you through an active GDB or OMIM session.

	Best of luck, and please contact me with suggestions for
improvements!

David Featherston

============================================================================
David Featherston
Research Geneticist &					CAOS/CAMM Center,
	Computational Genetics Consultant		P.O. Box 9010,
davidf@caos.kun.nl					6500 GL, Nijmegen
dwf11@phx.cam.ac.uk					The Netherlands
dfeather@hgmp.mrc.ac.uk					+31 (0)80 653383 tlf
http://www.caos.kun.nl/davidf.html			+31 (0)80 652977 FAX
	--------------------------------------------------------
	The CAOS/CAMM Center is the Dutch GDB Node & EMBnet Node
============================================================================

From owner-www@net.bio.net Tue Jan 17 22:00:00 1995
Newsgroups: bionet.software.www
Path: biosci!daresbury!bioftp.unibas.ch!moderate
From: perriere@misa.univ-lyon1.fr (Guy Perriere)
Subject: Annouce: B.subtilis database and server
Message-ID: <3fi3va$das@cismsun.univ-lyon1.fr>
Keywords: B.subtilis, Database, WWW server
Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland)
Organization: National Institute of Genetics
Date: Wed, 18 Jan 1995 04:03:53 GMT
Approved: bio-www@comp.bioz.unibas.ch
Lines: 84



            NRSUB: A NON-REDUNDANT DATA BASE FOR THE
                   BACILLUS SUBTILIS GENOME



I- Presentation

NRSub  (which  means  "Non  Redundant  Subtilis")  is a database
containing  a  "clean"  set of Bacillus subtilis sequences taken
from  the  SubtiList  collection. By "clean" we mean that all of
its nucleotide sequences are cleared of duplications. Additional
data  on  gene  mapping  and codon usage are also introduced, as
cross-references with EMBL, Swiss-Prot and Enzyme collections.

NRSub  release 4 contains a total of 248 contigs (61 composite).
All  these  sequences  are  chromosomal (plasmidic sequences are
removed)  and  totalize 1,251,557 bp. This represents approxima-
tively 30% of the entire Bacillus subtilis chromosome consisting
of  about 4,165 kbp. These sequences contain 1053 CDS (358 ORF),
72  tRNA  and  27  rRNA.  At  last, a total of 423 bibliographic
references can be accessed.


II- System requirement

NRSub  is provided either in EMBL flat file format or structured
under the ACNUC data base model. Of course, the flat file can be
used  with  any  kind  of computer. On the other hand, the ACNUC
version need the retrieval program query. We provide executables
of query for the following architectures: Sun Sparc (under SunOS
4.1.x  or Solaris 2.x), IBM RISC, SGI, and DEC Alpha. Sources of
the  line-mode  version  of  query  (in  Fortran and C) are also
included  in  the  distribution.  This line-mode  version may be
compiled  and ran on almost any UNIX system (BSD or SysV). To do
so, you need to have a Fortran compiler and a C compiler instal-
led on your computer.

Detailed instructions for set-up and use are given in the INSTALL
file of the package.


III- Distribution

The  release  4  of  NRSub is available at the NIG anonymous FTP
(ftp.nig.ac.jp  or  133.39.3.6)  in the directory /pub/db/nrsub.
It is also possible to access NRSub through a WWW server at URL: 

http://ddbjs4h.genes.nig.ac.jp/

The distribution includes: 

 - The  NRSub data base under ACNUC and the sources of the query
   program for line mode use (file NRSub.r4.tar.Z).

  - The flat version of the NRSub data base in EMBL format (file
    NRSub.dat or NRSub.dat.Z).

  - The  binaries  of the graphical version of the query program
    (files  query_win.*.Z).  Query_win.SUN file is for Sun Sparc
    under  SunOS,  query_win.SOL is for Sun Sparc under Solaris,
    query_win.RS6000  is  for  IBM  RISC, query_win.ALPHA is for
    DEC Alpha, and query_win.SGI is for Silicon Graphics.

All  the  *.Z  files  are  compressed  using  the  UNIX  command
'compress'.   In   a  way  to  uncompress  them,  you  must  use
'uncompress'.  The  flat  file  version  of NRSub is distributed
either compressed (NRSub.dat.Z) or in plain text (NRSub,dat) for
the people not working on a UNIX machine.

If  you  have some problems or questions, feel free to ask me at
the following address:

                 Guy Perriere
                 National Institute of Genetics
                 Shizuoka-ken 411, Mishima
                 Japan

                 Email: gperrier@ddbj.nig.ac.jp





From owner-www@net.bio.net Tue Jan 17 22:00:00 1995
Newsgroups: bionet.software.www
Path: biosci!daresbury!bioftp.unibas.ch!moderate
From: Gerard Manning
Subject: Virtual Library Web page for Drosophila
Message-ID: <1995Jan17.112215.19104@comp.bioz.unibas.ch>
Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland)
Organization: EMBnet Switzerland [Basel]
Date: Tue, 17 Jan 1995 11:22:15 GMT
Approved: bio-www@comp.bioz.unibas.ch
Lines: 18

[ Article crossposted from bionet.drosophila ]
[ Posted on Tue, 17 Jan 1995 03:06:10 GMT ]

The Virtual Library service for the World Wide Web now has a Drosophila page at

          http://www-leland.stanford.edu/~ger/drosophila.html

It's chief purpose is to act as a central source for all
Drosophila-related information on the net, be it FTP, World Wide Web or
Gopher. I will add some pages with basic Drosophila information as time
permits. If you know of any such resource which is not listed there, or if
you are interested in providing new information but don't know how please
contact me at the address below.

     Gerard Manning
     ger@leland.stanford.edu



From owner-www@net.bio.net Tue Jan 17 22:00:00 1995
Newsgroups: bionet.software.www
Path: biosci!daresbury!bioftp.unibas.ch!moderate
From: Shelley
Subject: Shoals Marine Laboratory WWW server
Message-ID: <1995Jan11.072315.25244@comp.bioz.unibas.ch>
Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland)
Organization: EMBnet Switzerland [Basel]
Date: Wed, 11 Jan 1995 07:23:15 GMT
Approved: bio-www@comp.bioz.unibas.ch
Lines: 19

[ Article crossposted from bionet.general ]
[ Posted on 10 Jan 1995 20:09:08 GMT ]

The Shoals Marine Laboratory (SML) is pleased to announce its World Wide
Web server.  You can use it to access information about our summer programs
in the marine sciences.  Operated jointly by Cornell University and the
University of New Hampshire, SML offers a diverse array of for-credit
college courses to undergraduate, graduate and high school students.  We
also have one-week "education vacation" options for those not interested in
college credit. Our URL is: http://www.sml.cornell.edu/Shoals/home.

Shelley Stuart
Shoals Marine Lab 
Cornell University

Phone:  607-255-3717
Email:  SHOALS-LAB@CORNELL.EDU



From owner-www@net.bio.net Thu Jan 19 22:00:00 1995
Newsgroups: bionet.software.www
Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!sunic!trane.uninett.no!daresbury!bioftp.unibas.ch!moderate
From: HOWARD_NEWSTADT.QM.YALE.EDU@news.ycc.yale.edu (HOWARD NEWSTADT)
Subject: YALE CENTER FOR ADVANCED INSTRUCTIONAL MEDIA HOME PAGE
Message-ID: <3fnje2$fv5@net.bio.net>
Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland)
Organization: YALE UNIVERSITY
Date: Fri, 20 Jan 1995 05:58:26 GMT
Approved: bio-www@comp.bioz.unibas.ch
Lines: 8


This address is an excellent gateway into a variety of CV topics and
programs.  Yale/AIM also offers several demos of cardiothoracic diognostic
imaging learning programs.


"http://info.med.yale.edu/caim/C_HOME.HTML"


From owner-www@net.bio.net Thu Jan 19 22:00:00 1995
Newsgroups: bionet.software.www
Path: biosci!daresbury!bioftp.unibas.ch!moderate
From: eggenber (Florian Eggenberger)
Subject: WWW Introduction: Part 18
Message-ID: <1995Jan18.104715.21166@comp.bioz.unibas.ch>
Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland)
Organization: EMBnet Switzerland [Basel]
Date: Wed, 18 Jan 1995 10:47:15 GMT
Approved: bio-www@comp.bioz.unibas.ch
Lines: 127


WWW INTRODUCTION        January 1995
================

PART 18: Glossary
-----------------

This is the eighteenth and final part of a series of postings describing 
the concept of the World-Wide Web and guiding anyone who is interested in 
obtaining and setting up the software required to access the Web.

The whole series is available on the newsgroup 
<A HREF = "news:bionet.software.www"> bionet.www.software </A> and
<A HREF = "news:unibas.seminars"> unibas.seminars </A>. Both an 
<A HREF = "http://www.ch.embnet.org/bio-www/archive/florianW3_1.html">
English </A> and a
<A HREF = "http://www.ch.embnet.org/bio-www/archive/florianW3_sp.html">
Spanish </A> version (contributed by Pablo Liendo, Venezuela), can be also 
accessed via the
<A HREF = "http://www.ch.embnet.org/bio-www/info.html">
WWW archive </A> of the newsgroup bionet.www.software.

The World-Wide Web has its own terminology. Here is a brief explanation of 
terms used in previous parts of this introduction:

AIX - UNIX based operating system developed by IBM

Anonymous FTP - FTP that allows the retrieval of files from public sites

Archie - a network tool that searches anonymous FTP sites for files

ASCII - American Standard Code for Information Interchange

BITNET - "Because It's Time Network", an academic collective of networks

Browser - a client allows access to the World-Wide Web

CERN - European Centre for Particle Physics, Switzerland

Client - a program that can request services from a server via the network

Domain - a naming category in the DNS

DNS - Domain Name System, hierarchical system of host naming

Driver - a program that controls an external device or an I/O port

EARN - European Academic Research Network

EMBnet - European Molecular Biology Network

Ethernet - standard for physical and data link layer specifications

FTP - File Transfer Protocol, Internet standard for transferring files

Gopher - network tool that allows to access various types of data

Host - a computer that acts as a client or a server

HTML - Hypertext Markup Language, standard language of WWW

HTTP - Hypertext Transfer Protocol, standard protocol of WWW

Hypermedia - multimedia hypertext

Hyperlink - relationship between two objects on the Web

Hypertext - text that contains pointers to other text

Interrupt - a request-for-attention signal

IP - the standard Internet Protocol

Internet - international collective of networks running TCP/IP

IRIX - UNIX-based operation system developed by SGI

LAN - Local Area Network

NNTP - News Network Transfer Protocol, method to transfer News articles

Packet - a network message with header, addressing information and data

Protocol - the rules two computers must follow to exchange messages

Server - a program that provides a service to a client

SLIP - Serial Line Internet Protocol

SMTP - Simple Mail Transfer Protocol

Subnet - a LAN within an internetwork

TCP/IP - Transmission Control Protocol / Internet Protocol

TELNET - Internet standard protocol for remote terminal connection

ULTRIX - UNIX-based operating system developed by DEC

UNIX - operating system developed by Bell Laboratories

URL - Uniform Resource Locator

VM - operating system developed by IBM

VMS - operating system developed by DEC

WAIS - Wide Area Information Server



ACKNOWLEDGEMENTS
----------------

EMBnet Switzerland is a project funded by the University of Basel, the 
Swiss National Science Foundation, and industrial contributions from 
Digital Equipment and Silicon Graphics (in alphabetical order).


-- 
+------------------------------+--------------------------------+
|  F. Eggenberger, Ph.D.       |  eggenber@comp.bioz.unibas.ch  |
|  Biocomputing                |  eggenberger1@ubaclu.unibas.ch |        
|  University of Basel         |  Fax  +41 / 61 267 20 78       | 
|  Switzerland                 |  Tel  +41 / 61 267 22 47       | 
+------------------------------+--------------------------------+


From owner-www@net.bio.net Sun Jan 22 22:00:00 1995
Newsgroups: bionet.software.www
Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!sunic!trane.uninett.no!daresbury!bioftp.unibas.ch!moderate
From: solovyev@cmb.bcm.tmc.edu (Victor V. Solovyev)
Subject: Gene-Finder, SS predic. by WWW Mosaic and Email servers
Message-ID: <199501210019.SAA10761@falcon.cellb.bcm.tmc.edu>
Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland)
Organization: EMBnet Switzerland [Basel]
Date: Sat, 21 Jan 1995 00:19:24 GMT
Approved: bio-www@comp.bioz.unibas.ch
Lines: 52

Email servers and WWW Mosaic:
===============================
	BCM Gene-finder and secondary structure prediction
programs are available now by sending the file containing 
a sequence (the sequence format is described in Help files) to

The University of Houston Gene server:
service@bchs.uh.edu or

Weizmann University server:
services@bioinformatics.weizmann.ac.il
     with the subject line "program_name". 

Examples: mail -s fgeneh service@bchs.uh.edu < test.seq
mail -s fgeneh services@bioinformatics.weizmann.ac.il < test.seq

You can obtain help files by sending the subject line
        man <servicename> such as
        Subject: man hexon to    service@bchs.uh.edu

Help files now you can read from WWW Mosaic:

URL:http://kiwi:8088/search-launcher/launcher.html

  BCM Gene Finder 
  BCM protein secondary structure prediction 

or: directly:

http://dot:9331/gene-finder/gf.html   (HELP and RUN HEXON)

http://dot:9331/pssprediction/pssp.html (Help and RUN)

      The Baylor College Of Medicine Computational Biology Group
                             Houston, TX

The services are 

FGENEH - search for gene structure with exons assembling by dynamic programming 
FEXH   - search for 5'-, internal and 3'-exons
HEXON  - search for internal exons 
HSPL   - search for splice sites


SSP    - prediction of a-helix and b-strand in globular proteins
	 by segment-oriented approach.
NSSP   - prediction of a-helix and b-strand segments in globular proteins
         by nearest-neighbor algorithm.

Problems, comments, and suggestions:
   Can be mailed to solovyev@cmb.bcm.tmc.edu.


From owner-www@net.bio.net Sun Jan 22 22:00:00 1995
Newsgroups: bionet.software.www
Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!Germany.EU.net!EU.net!sunic!trane.uninett.no!daresbury!bioftp.unibas.ch!moderate
From: rsmith@DOT.IMGEN.BCM.TMC.EDU (Randall Smith)
Subject: New BCM WWW database search services
Message-ID: <RSMITH.95Jan20165059@dot.bcm.tmc.edu>
Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland)
Organization: Institute for Molecular Genetics, Baylor College of Medicine
Date: Fri, 20 Jan 1995 22:50:59 GMT
Approved: bio-www@comp.bioz.unibas.ch
Lines: 51


The Human Genome Center along with the Molecular Biology Computer
Resource, Baylor College of Medicine, would like to announce several
new WWW database search services which we are making available for
beta-testing via our new 'BCM Search Launcher' Web page:

http://kiwi.imgen.bcm.tmc.edu:8088/search-launcher/launcher.html


The BCM Search Launcher organizes molecular biology-related search and
analysis services available on the WWW by function, and provides a
single point-of-entry for related searches (e.g., a single page for
launching protein sequence searches using standard parameters).


New search services available for beta-testing include:

1) BEAUTY (BLAST Enhanced Alignment Utility), an enhanced version of
the NCBI's BLAST database search tool.  BEAUTY, when used in
conjunction with two new sequence databases that we have developed,
incorporates information on sequence family membership, the location
of the conserved domains, and the locations of any annotated domains
and sites directly into BLAST search results.  These enhancements make
it much easier to detect weak, but functionally significant, matches
in BLAST database searches.

A more detailed program description, as well as a description of the
Protein Family and Conserved Regions databases used in this program is
available at:

http://dot.imgen.bcm.tmc.edu:9331/seq-search/Help/beauty.html


2) NCBI BLAST Searches with Entrez and SRS Links

The BCM Search Launcher also includes a new interface that adds NCBI
Entrez and Sequence Retrieval System (SRS) links to BLAST search
results returned by the NCBI's WWW BLAST Server.  These additional
links can be extremely useful when analyzing BLAST search results.


------------------------------------------------------------------------
Randall F. Smith
Human Genome Center
Department of Molecular and Human Genetics and
W.M. Keck Center for Computational Biology
Baylor College of Medicine, Houston, TX  77030  USA

rsmith@bcm.tmc.edu; 713-798-4735; FAX: 713-798-5386
------------------------------------------------------------------------


From owner-www@net.bio.net Mon Jan 23 22:00:00 1995
Newsgroups: bionet.software.www
Path: biosci!daresbury!bioftp.unibas.ch!moderate
From: Reinhard Doelz <doelz@biox.embnet.unibas.ch>
Subject: CALL FOR CONTRIBUTIONS: WWW IN BIOLOGY
Message-ID: <1995Jan24.065429.28555@comp.bioz.unibas.ch>
Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland)
Organization: EMBnet Switzerland [Basel]
Date: Mon, 23 Jan 1995 18:55:22 GMT
Approved: bio-www@comp.bioz.unibas.ch
Lines: 66

<H3><a href=http://www.igd.fhg.de/www95.html> 

                    Third International World-Wide Web Conference
                       Technology, Tools, and Applications
                      April 10-14, 1995, Darmstadt, Germany

</a></H3><HR><a href=http://www.igd.fhg.de/www/www95/igdhome.html>
  Organizer: Fraunhofer Institute for Computer Graphics in Darmstadt, Germany.
</a><pre>


          w o r k s h o p   e:   b i o l o g y   o n    t h e    w e b 
-----------------------------------------------------------------------------
                   C A L L   F O R   C O N T R I B U T I O N S 

Half-day workshop on Monday, April 10, 1995          2.00 p.m. - 5.30 p.m.

</pre><HR><a href=ftp://bioftp.unibas.ch/archive_data/www-bio.html><pre>

Since the conference in 1994 at Geneva, the demand for WWW applications in
Biology is rising steadily, and new applications show up instantaneously. 
</pre></a>
Two areas of interest will be tackled specifically: 
<MENU>
<LI>AREA A:
   Biology and the Web - Getting scientific data from a General Purpose
   Information System. How to fully accommodate today's applications. 
<LI>AREA B: 
   Scientists and their views - Different data and methods cause different
   displays of similar conclusions. How can the scientists unite responses
   from different sources? 
</MENU>

   The approaches chosen to expand on Areas A or B might include
   contributions on: 
<UL>
<LI>      Resource discovery: Maintenance of meta lists 
<LI>      Redundancy: How to approach the 'best' of some very similar servers 
<LI>      State of the Art WWW servers: Approaches and problems 
<LI>      Database synchronization on the Web via the Web 
</UL>

The workshop is open to everyone agreeing to contribute a short (less
   than 4 pages) paper or written participant statement. We want to have
   active participants in the workshops. The workshop chairs will decide
   on the program and presentations. Depending on the number of
   contributing participants the workshop may be opened also for
   additional non-contributing participants.
<pre>
   Please send your contribution directly to the workshop chairs no later
   than March 1: 

   Reinhard Doelz 
      Biocomputing | Biozentrum der Universitdt Basel
      Basel, Switzerland
      Email: doelz@ubaclu.unibas.ch
      Fax: +41-61-267-2078 




-- 
 R.Doelz         Klingelbergstr.70| Tel. x41 61 267 2247  Fax x41 61 267 2078|
 Biocomputing        CH 4056 Basel| electronic Mail    doelz@ubaclu.unibas.ch|
 Biozentrum der Universitaet Basel|-------------- Switzerland ---------------|
<a href=http://beta.embnet.unibas.ch/>EMBnet Switzerland:info@ch.embnet.org</a> 

From owner-www@net.bio.net Mon Jan 23 22:00:00 1995
Newsgroups: bionet.software.www
Path: biosci!daresbury!bioftp.unibas.ch!moderate
From: FlyBase Project Members <flybase@morgan.harvard.edu>
Subject: FlyBase WWW Home Page
Message-ID: <1995Jan24.070843.28878@comp.bioz.unibas.ch>
Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland)
Organization: EMBnet Switzerland [Basel]
Date: Mon, 23 Jan 1995 22:12:52 GMT
Approved: bio-www@comp.bioz.unibas.ch
Lines: 45

			FlyBase WWW Home Page

   FlyBase is pleased to announce public availability of a fully
developed WWW home page for exploring and searching the FlyBase database
of genetic information about Drosophila.

     The URL you can use to reach the FlyBase home page is

http://morgan.harvard.edu/

     The FlyBase home page offers several new capabilities.

    Many of the reports you can request as the result of a search include
WWW hyperlinks to the WWW pages for such cross-referenced databases as
the sequence databases and Medline.

     The most notable new feature is called CytoSearch, a search
tool that enables users to create customized cytogenetic maps of any
desired region of the genome.  You can specify the region as well as
the types of genetic entities (e.g., genes, transposons, aberrations, 
clones) you wish to have listed for that region.  To get to CytoSearch, 
select CytoSearch on the page that comes up when you select FlyBase Data 
Access on the main home page.  It is also possible to reach CytoSearch 
by selecting New FlyBase Search Tools on the home page.  Be sure to read 
the CytoSearch help document if you wish to take full advantage of these 
powerful searches.

    The FlyBase Data Access page also provides gopher+ access to the
FlyBase server.  All gopher+ search forms as well as the forms for
updating your address or ordering stocks from the Bloomington stock
center are fully functional.  The Gopher+ WWW relay we are providing does
not yet know how to offer you multiple report forms for gopher+ search
results, so if you require search results in rtf format, you should
continue to use a gopher+ client to request them.

    You can use the Contact FlyBase choice on the home page to make
inquiries or report problems to flybase-help@morgan.harvard.edu, or to
send updates and corrections to the information in FlyBase to
flybase-updates@morgan.harvard.edu.  If you contact us for help, please
indicate which WWW browser (Mosaic, Netscape, Lynx, something else) and
what sort of computer you were using.  This will help us to provide you
with tools that meet your needs.

    As before, you can continue to use gopher or gopher+ clients to 
access FlyBase. 

From owner-www@net.bio.net Thu Jan 26 22:00:00 1995
Newsgroups: bionet.software.www
Path: biosci!bcm!cs.utexas.edu!swrinde!howland.reston.ans.net!pipex!sunic!trane.uninett.no!daresbury!bioftp.unibas.ch!moderate
From: moderate (Bio-WWW moderator @ EMBnet Switzerland)
Subject: [aministrativa]
Message-ID: <1995Jan27.182446.27056@comp.bioz.unibas.ch>
Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland)
Organization: EMBnet Switzerland [Basel]
Date: Fri, 27 Jan 1995 18:24:46 GMT
Approved: bio-www@comp.bioz.unibas.ch
Lines: 8

Apologies - we did have a crash of the news system recently. We're catching 
up over the weekend but some articles have been sent multiple times. 

Regards
Reinhard Doelz
bio-www moderator



From owner-www@net.bio.net Thu Jan 26 22:00:00 1995
Newsgroups: bionet.software.www
Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!sunic!ugle.unit.no!trane.uninett.no!daresbury!bioftp.unibas.ch!moderate
From: Betty K Mansfield (615)576-6669
Subject: Human Genome News, etc. on WWW at Oak Ridge National Laboratory
Message-ID: <1995Jan25.062647.3684@comp.bioz.unibas.ch>
Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland)
Organization: EMBnet Switzerland [Basel]
Date: Wed, 25 Jan 1995 06:26:47 GMT
Approved: bio-www@comp.bioz.unibas.ch
Lines: 41

[ Article crossposted from bionet.molbio.genome-program ]
[ Posted on 24 Jan 1995 14:43:29 -0800 ]

         
Human Genome News, a bimonthly newsletter about the Human Genome Project, is
available through World Wide Web at
http://www.ornl.gov/TechResources/Human_Genome/home.html. Jointly sponsored
by the human genome programs of the National Institutes of Health and U.S.
Department of Energy, HGN includes technical and general interest articles
about progress toward project goals, meeting reports, national and
international project news, bioinformatics and laboratory research
resources, genome event and training calendars, and grant and fellowship
announcements. 

Also accessible at the same WWW site are occasional in-depth meeting
reports, a list of chromosome-mapping editors, contact information for NIH
and DOE project staff, information on genome centers, selected genome
resources, DOE human genome program reports, a link to the DOE genetics
primer, and pointers to other sites relevant to molecular biology research,
including the home pages of the DOE Human Genome Program and NIH. 

For a hard copy subscription to HGN, fill out the form on the WWW server or
contact Betty Mansfield at Human Genome Management Information System; Oak
Ridge National Laboratory; 1060 Commerce Park, MS 6480; Oak Ridge, TN 37830
(615/576-6669, Fax: /574-9888, Internet: mansfieldbk@ornl.gov).

        HGN is also available on the Johns Hopkins Gopher at gopher.gdb.org

        HGMIS staff welcomes suggestions and inquiries for additional
information.

Betty K. Mansfield
Task leader, Human Genome Management Information System
Oak Ridge National Laboratory
1060 Commerce Park, MS 6480
Oak Ridge, TN  37830
615/576-6669; Fax: 615/574-9888; Email: bkq@ornl.gov

                HGMIS World Wide Web URL:
http://www.ornl.gov/TechResources/Human_Genome/home.html


From owner-www@net.bio.net Thu Jan 26 22:00:00 1995
Newsgroups: bionet.software.www
Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!sunic!ugle.unit.no!trane.uninett.no!daresbury!bioftp.unibas.ch!moderate
From: Betty K Mansfield (615)576-6669
Subject: Human Genome News, etc. on WWW at Oak Ridge National Laboratory
Message-ID: <1995Jan27.170522.24305@comp.bioz.unibas.ch>
Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland)
Organization: EMBnet Switzerland [Basel]
Date: Wed, 25 Jan 1995 06:26:47 GMT
Approved: bio-www@comp.bioz.unibas.ch
Lines: 41

[ Article crossposted from bionet.molbio.genome-program ]
[ Posted on 24 Jan 1995 14:43:29 -0800 ]

         
Human Genome News, a bimonthly newsletter about the Human Genome Project, is
available through World Wide Web at
http://www.ornl.gov/TechResources/Human_Genome/home.html. Jointly sponsored
by the human genome programs of the National Institutes of Health and U.S.
Department of Energy, HGN includes technical and general interest articles
about progress toward project goals, meeting reports, national and
international project news, bioinformatics and laboratory research
resources, genome event and training calendars, and grant and fellowship
announcements. 

Also accessible at the same WWW site are occasional in-depth meeting
reports, a list of chromosome-mapping editors, contact information for NIH
and DOE project staff, information on genome centers, selected genome
resources, DOE human genome program reports, a link to the DOE genetics
primer, and pointers to other sites relevant to molecular biology research,
including the home pages of the DOE Human Genome Program and NIH. 

For a hard copy subscription to HGN, fill out the form on the WWW server or
contact Betty Mansfield at Human Genome Management Information System; Oak
Ridge National Laboratory; 1060 Commerce Park, MS 6480; Oak Ridge, TN 37830
(615/576-6669, Fax: /574-9888, Internet: mansfieldbk@ornl.gov).

        HGN is also available on the Johns Hopkins Gopher at gopher.gdb.org

        HGMIS staff welcomes suggestions and inquiries for additional
information.

Betty K. Mansfield
Task leader, Human Genome Management Information System
Oak Ridge National Laboratory
1060 Commerce Park, MS 6480
Oak Ridge, TN  37830
615/576-6669; Fax: 615/574-9888; Email: bkq@ornl.gov

                HGMIS World Wide Web URL:
http://www.ornl.gov/TechResources/Human_Genome/home.html


From owner-www@net.bio.net Thu Jan 26 22:00:00 1995
Newsgroups: bionet.software.www
Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!sunic!ugle.unit.no!trane.uninett.no!daresbury!bioftp.unibas.ch!moderate
From: Betty K Mansfield (615)576-6669
Subject: Human Genome News, etc. on WWW at Oak Ridge National Laboratory
Message-ID: <1995Jan27.165823.23548@comp.bioz.unibas.ch>
Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland)
Organization: EMBnet Switzerland [Basel]
Date: Wed, 25 Jan 1995 06:26:47 GMT
Approved: bio-www@comp.bioz.unibas.ch
Lines: 41

[ Article crossposted from bionet.molbio.genome-program ]
[ Posted on 24 Jan 1995 14:43:29 -0800 ]

         
Human Genome News, a bimonthly newsletter about the Human Genome Project, is
available through World Wide Web at
http://www.ornl.gov/TechResources/Human_Genome/home.html. Jointly sponsored
by the human genome programs of the National Institutes of Health and U.S.
Department of Energy, HGN includes technical and general interest articles
about progress toward project goals, meeting reports, national and
international project news, bioinformatics and laboratory research
resources, genome event and training calendars, and grant and fellowship
announcements. 

Also accessible at the same WWW site are occasional in-depth meeting
reports, a list of chromosome-mapping editors, contact information for NIH
and DOE project staff, information on genome centers, selected genome
resources, DOE human genome program reports, a link to the DOE genetics
primer, and pointers to other sites relevant to molecular biology research,
including the home pages of the DOE Human Genome Program and NIH. 

For a hard copy subscription to HGN, fill out the form on the WWW server or
contact Betty Mansfield at Human Genome Management Information System; Oak
Ridge National Laboratory; 1060 Commerce Park, MS 6480; Oak Ridge, TN 37830
(615/576-6669, Fax: /574-9888, Internet: mansfieldbk@ornl.gov).

        HGN is also available on the Johns Hopkins Gopher at gopher.gdb.org

        HGMIS staff welcomes suggestions and inquiries for additional
information.

Betty K. Mansfield
Task leader, Human Genome Management Information System
Oak Ridge National Laboratory
1060 Commerce Park, MS 6480
Oak Ridge, TN  37830
615/576-6669; Fax: 615/574-9888; Email: bkq@ornl.gov

                HGMIS World Wide Web URL:
http://www.ornl.gov/TechResources/Human_Genome/home.html


From owner-www@net.bio.net Thu Jan 26 22:00:00 1995
Newsgroups: bionet.software.www
Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!sunic!ugle.unit.no!trane.uninett.no!daresbury!bioftp.unibas.ch!moderate
From: BIOSCI Administrator <biosci-help@net.bio.net>
Subject: IMPORTANT ANNOUNCEMENT - BIOSCI/bionet WWW HOME PAGE
Message-ID: <1995Jan27.171610.24491@comp.bioz.unibas.ch>
Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland)
Organization: EMBnet Switzerland [Basel]
Date: Thu, 26 Jan 1995 19:41:35 GMT
Approved: bio-www@comp.bioz.unibas.ch
Lines: 26

I am please to announce the availability of the BIOSCI/bionet
newsgroups World Wide Web home page at URL 

			 http://www.bio.net/

The BIOSCI home page will also be mirrored at our Daresbury site in
the near future.

The home page currently provides easy access to BIOSCI documentation
and another route (besides FTP, WAIS, and gopher) into the
BIOSCI/bionet newsgroup archives, journal Table of Contents index, and
our indexed address database of biologists on the network (currently
over 5,200 entries).  Other services will be added to the Web page in
the future, not the least of which will be access to pictures of the
BIOSCI staff (flamers, take note! - suitable for framing on your dart
board or for use in other amusements 8-) ... perhaps we should start a
"Biologists' Network Hall of Flame" 8-).

Please address comments/suggestions to biosci-help@net.bio.net.

				Sincerely,

				Dave Kristofferson
				BIOSCI/bionet Manager

				biosci-help@net.bio.net

From owner-www@net.bio.net Sun Jan 29 22:00:00 1995
Newsgroups: bionet.software.www
Path: biosci!daresbury!bioftp.unibas.ch!moderate
From: Leon Avery
Subject: WBG 13(5)
Message-ID: <1995Jan30.073014.20577@comp.bioz.unibas.ch>
Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland)
Organization: EMBnet Switzerland [Basel]
Date: Fri, 27 Jan 1995 11:35:45 GMT
Approved: bio-www@comp.bioz.unibas.ch
Lines: 18

[ Article crossposted from bionet.celegans ]
[ Posted on 25 Jan 1995 16:06:09 -0800 ]

The Table of Contents of the February 1, 1995 issue of the Worm
Breeder's Gazette is now available on the CGC gopher server
(elegans.cbs.umn.edu) and Avery Lab WWW server
(http://eatworms.swmed.edu/). The text of 37 articles submitted by
e-mail (from a total of 84) is also available at the WWW site. There
is even one article that was submitted by e-mail but not on paper! The
text is also available as a single compressed file. (Use the "Load To
Local Disk" option of your WWW browser.)

-- 
Leon Avery					   (214) 648-2420 (office)
Department of Biochemistry			            -2768 (lab)
University of Texas Southwestern Medical Center             -8856 (fax)
5323 Harry Hines Blvd				   leon@eatworms.swmed.edu
Dallas, TX  75235-9038			  http://eatworms.swmed.edu/~leon/

From owner-www@net.bio.net Sun Jan 29 22:00:00 1995
Newsgroups: bionet.software.www
Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!warwick!news.dcs.warwick.ac.uk!hgmp.mrc.ac.uk!daresbury!bioftp.unibas.ch!moderate
From: "Victor V. Solovyev" <solovyev@cmb.bcm.tmc.edu>
Subject: Local URL for WWW GeneFinder and sec.str.pred. was posted
Message-ID: <1995Jan30.090337.22827@comp.bioz.unibas.ch>
Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland)
Organization: EMBnet Switzerland [Basel]
Date: Thu, 26 Jan 1995 00:14:24 GMT
Approved: bio-www@comp.bioz.unibas.ch
Lines: 9

  Please, use WWW BCM Human Genome Center and Search launcher 
          Home page

URL:http://kiwi.imgen.bcm.tmc.edu:8088/search-launcher/launcher.html

for accsess to Gene-Finder and Secondary structure prediction 
Help files and programs.

Thank you, Victor Solovyev

From owner-www@net.bio.net Sun Jan 29 22:00:00 1995
Newsgroups: bionet.software.www
Path: biosci!daresbury!bioftp.unibas.ch!moderate
From: FlyBase Project Members <flybase@morgan.harvard.edu>
Subject: More FlyBase URLs for Linking
Message-ID: <1995Jan30.075716.21413@comp.bioz.unibas.ch>
Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland)
Organization: EMBnet Switzerland [Basel]
Date: Mon, 30 Jan 1995 01:10:05 GMT
Approved: bio-www@comp.bioz.unibas.ch
Lines: 71

     At the beginning of last week we announced the URL for the FlyBase
home page on the World Wide Web.  The purpose of this followup
announcement is to provide others maintaining their own WWW pages with
two additional URL's that help them set up hyperlinks to FlyBase.

     As previously announced, the main URL for the FlyBase home page is

http://morgan.harvard.edu/

     There are two additional kinds of URLs already in place that WWW
page maintainers may find useful to link to.  If you would like assistance
in setting up links to these sorts of URL's for FlyBase, please email us
at flybase-help@morgan.harvard.edu.  If you would like to use types of
links not described here, send us email; there are many other sorts of
public links we could provide if there are database and WWW page maintainers
who would make use of them.

     The first URL is a link to the script that returns fully hyperlinked
FlyBase gene reports:

http://morgan.harvard.edu/htbin-post/gene.script?

You can link to this script with either a correctly capitalized FlyBase
gene symbol or FBgn number (FlyBase gene number) for that gene.  For
example the Drosophila gene that currently has the symbol Adf1 has been
assigned the permanent FlyBase gene number FBgn0000054, so you can link
to it using the URL:

http://morgan.harvard.edu/htbin-post/gene.script?FBgn0000054

We do not encourage you to use the gene symbol to link to the gene,
since gene symbols are subject to change for a variety of reasons, such
as when two or more groups of alleles are discovered to be alleles of one 
and the same gene.

     You can see examples of such interdatabase links using FlyBase gene
numbers in action by selecting a Drosphila SWISS-PROT entry on the ExPASy
Molecular Biology Server at URL

http://expasy.hcuge.ch/


     The second FlyBase link of interest is the URL for the gopher+
capable relay to the top of the FlyBase gopher server:

http://morgan.harvard.edu/htbin-post/flybase?top/

     If you wish, you can link to one of the top-level FlyBase
gopher directories by naming it.  To get to the stocks directory, use

http://morgan.harvard.edu/htbin-post/flybase?top?stocks

     You can even name locations in deeper directories, such as

http://morgan.harvard.edu/htbin-post/flybase?top?stocks/stock-centers/bloomington

but we recommend against this practice, since it is not unusual for 
details of the directory names and organization to change from time
to time.


     Finally, it should be mentioned for anyone putting FlyBase URLs in
their hotlists or setting up FlyBase WWW links that you should not rely
on the more detailed URLs continuing to work.  The simple forms
recommended here will be supported, but we can make no promises that URLs
that list several directory levels will be.  

     Please let us know if you link to any of the FlyBase URLs and
send reports of any problems you encounter in doing so to     

flybase-help@morgan.harvard.edu

From owner-www@net.bio.net Sun Jan 29 22:00:00 1995
Newsgroups: bionet.software.www
Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!pipex!warwick!news.dcs.warwick.ac.uk!hgmp.mrc.ac.uk!daresbury!bioftp.unibas.ch!moderate
From: Georg Fuellen <fuellen@techfak.uni-bielefeld.de>
Subject: WANTED: Consulting Students and Instructors for Internet Biocomputing Course !!
Message-ID: <1995Jan30.091932.23309@comp.bioz.unibas.ch>
Sender: moderate@comp.bioz.unibas.ch (Bio-WWW moderator @ EMBnet Switzerland)
Organization: EMBnet Switzerland [Basel]
Date: Fri, 27 Jan 1995 17:12:45 GMT
Approved: bio-www@comp.bioz.unibas.ch
Lines: 309


If you're interested in the Internet Biocomputing Course,
as a student or online instructor, please read on !!

A similar message has just been sent to all people who have 
already expressed an interest in attending the course in Summer 1995.
You are invited to join.

>>>>
Dear Prospective Student,
Dear Collaborator,

Our effort has made good progress, which you can examine by pointing
your hypertext browser to our homepage,
http://www.techfak.uni-bielefeld.de/techfak/persons/fuellen/BCChome.html
[[ Our US mirror is
http://www.mit.edu:8001/afs/athena/user/f/u/fuellen/News/Ga/REM/Gna/BCChome.html
Please visit our homepage before sending inquiries; we're currently busy with
writing the hypertext book, and a response may take some time. ]]
You may wish to subscribe yourself to our moderated (ca. 5 posts/YEAR)
"Biocomputing Course Updates" mailing list, by sending a message to 
majordomo@hrz.uni-bielefeld.de, with no subject line, and the following 
message body:
subscribe vsns-bcd-updates
You will be subscribed to a minimum traffic mailing list that keeps you 
informed about our progress, e.g. the availability of our hypertext book, 
and the beginning of student registration.

We are now looking for "Consulting Students", i.e. students who are
guaranteed admission in return for helping us in technical and administrative
matters. If you're seriously interested in any of these "jobs", please
contact the course coordinator, vsns-bcd-admcoord@techfak.uni-bielefeld.de
(Georg Fuellen) as soon as possible !

Enrollment into the course may be limited to ca. 30 students (depending
on the availability of instructors), so this is your excellent chance
for getting a free ticket to an exciting, cutting-edge learning 
experience in biocomputing ! If you'd like to attend, but you feel
that none of the following jobs suits you, pls keep watching our homepage,
and/or subscribe yourself to our moderated "Prospective Students" mailing list,
by sending a message to majordomo@hrz.uni-bielefeld.de,
with no subject line, and the following message body:
subscribe vsns-bcd-prospective 
You will be subscribed to a moderated mailing list that keeps you informed 
about new "job" opportunities, questionaires, and the beginning of registration.

See below for "Advanced Jobs" (e.g. Instructor), our DISCLAIMER, and our 
GNA Course Catalog entry.


"Consulting Student" Jobs
=========================
=========================

"Job" #BCD-95-04
"MOO programmer" (2-3 positions)
================================

You will modify and enhance the VSNS-PPS electronic classroom at BioMOO, 
developing a classroom suitable for our course. Note: MOO programming is 
nothing sophisticated ! Even High-School teens with some experience in Pascal
(or some other structured programming language) have learned it in a few 
weeks.

You need: MOO experience. You can attend a MOO programming course
for free, if you do not yet have MOO programming experience.

Your benefit: You are admitted to the course as a "Consulting
Student".  Large part of your work helps you directly in your
understanding of Biocomputing, and MOO coding.

"Job" #BCD-95-11
"Mirroring Coordinator"
=======================

You will take care of the proper mirroring of our course material (Hypertext
tree). You will work together with the system administrators of various
WWW-sites that have offered to mirror the course material.
See http://www.techfak.uni-bielefeld.de/techfak/persons/fuellen/Book/mirroring.html
for more details.

You need: HTML/http experience. Forms/CGI experience useful.

Your benefit: You are admitted to the course as a "Consulting
Student".  You will learn a lot about hypertext from the server side.

"Job" #BCD-95-12
"External Resource Manager"
===========================

You will take care that the external resources used by our course
are stable. To this end, a letter shall be sent to all people who offer 
resources that shall be used by our course. You will start with the resources 
mentioned in our Master Outline (see homepage). If authors add external 
resources, they will ask you to deal with these new resources in the same way. 
In a few cases, you may need to track down the maintainer of a page, in order
to email him/her.
You're encouraged to discover useful resources on your own !!
See http://www.techfak.uni-bielefeld.de/techfak/persons/fuellen/Book/externRes.html
for more details.

You need: WWW/Internet experience.

Your benefit: You are admitted to the course as a "Consulting
Student". You will learn a lot more about Internet/WWW.

"Job" #BCD-95-05
"Question Authority"
====================

More info: You will be the first person to talk to if students or
other people have questions of a technical or administrative matter. 
You will forward the more difficult questions to specialized mailing 
lists, or the course coordinator.

You need: Good communication skills, willingness to get a good overview 
about what's going on in the course, and to use the MOO.

Your benefit: You are admitted to the course as a "Consulting
Student".  Large part of your work helps you directly in your
understanding of Online Distance Education.

"Job" #BCD-95-01
"Assistance with HTML document preparation I"
=============================================

More info: You will assist one of our authors to translate 
documents perepared via PC based MS Word 6.2 to HTML. You may need
to find and install an automatic conversion program. 
Alternatively, if the author agrees, you will introduce him
to writing simple HTML, and take care of more complex features (equations, 
tables etc) yourself. 

You need: Knowledge of HTML, and (likely) MS Word 6.2.

Your benefit: You are admitted to the course as a "Consulting
Student". Your assistance will be acknowledged in the foreword
of the hypertext book, and possibly CD-ROM.

"Job" #BCD-95-02
"Assistance with HTML document preparation II"
==============================================

More info: Similar to "Assistance with HTML document preparation I",
but you need some experience w/ LaTex, instead of MS Word 6.2.

"Job" #BCD-95-06
"Glossary curator and administrator"
====================================

More info:  see Newsletter Vol.1 No.2, available via our homepage.
You will use technology prepared for Peter Murray-Rust's Protein Structure 
course, in order to generate and maintain a hypertext glossary of
Biocomputing terms. Most/All entries will be provided by the authors.

You need: Knowledge of HTML.

Your benefit: You are admitted to the course as a "Consulting
Student". Large part of your work helps you directly in your 
understanding of Biocomputing.

"Job" #BCD-95-07
"Development and Evaluation of questionaires sent to all students"
===================================================================

More info: In cooperation with the organizers, you will 
develop an email (or, possibly, HTML-Forms-based)
questionaire to be sent to all prospective students. It will aid
the registration process, and tell the authors/instructors more 
about the skills and needs of the students. You will report your findings 
to the Faculty. Possibly, you will also organize mid-term and final
questionaires.

You need: Knowledge of HTML helpful.

Your benefit: You are admitted to the course as a "Consulting
Student". Large part of your work helps you directly in your
understanding of Online Distance Education, and Biocomputing.

"Job" #BCD-95-08
"Development of Self-Assessment Forms" (2-3 positions)
======================================================

More info: You will use technology prepared for Peter Murray-Rust's
Protein Structure course, in order to generate and maintain Self-Assessment 
Forms for the other students.

You need: Knowledge of HTML.

Your benefit: You are admitted to the course as a "Consulting
Student". Large part of your work helps you directly in your 
understanding of Biocomputing.


Advanced Jobs
=============
=============

"Job" #BCD-95-09
"Instruction May-July 1995, ca. 11 weeks." (2-6 positions)
==========================================================

Instructors are still needed. See our homepage for details, and get in
contact with fuellen@dali.mathematik.uni-bielefeld.de (Georg Fuellen).
See our Mission Statement, paragraph "2.", for further details about the 
instructor's job. (The Mission Statement is available via our homepage.)

"Job" #BCD-95-10
"Organize On-line Plenary Discussions at BioMOO"
================================================

More info: Via usenet/bionet and BioMOO, you will solicit 
(self-)nominations of possible participants in the discussions
about Standards, Ethics, and the "Future of Biocomputing"
(for more details, see the end of the Unified Master Outline,
which is available via our homepage).
For the "Standards" and "Ethics" discussions,
you will look for author(s) of a rather short preperatory
document, which shall also be included into our hypertext book.
You will report to the faculty a list of suggestions for
possible attendies. You will not bear any responsibility for the
outcome of the discussions :-)
You will organize date & time of the plenary discussion.
You may need to train some attendies in using the MOO.

You need: Good communication skills, good overview about the
course, willingness to use the MOO. HTML helpful.

Your benefit: If you like, you are admitted to the course as a "Consulting
Student". This job is also a perfect way of getting into contact with
lots of interesting ppl.

===============
===============

Our disclaimer:

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 IN NO EVENT SHALL THE GLOBEWIDE NETWORK ACADEMY, THE VIRTUAL SCHOOL OF NATURAL
 SCIENCES, BIOMOO, OR ANY OTHER PARTICIPATING VOLUNTEER BE LIABLE TO ANY PARTY
 FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING
 OUT OF THE PARTICIPATION IN THIS CLASS, AND/OR OUT OF THE USE OF THE
 INFORMATION PROVIDED IN THIS CLASS, EVEN IF THE GLOBEWIDE NETWORK ACADEMY,
 THE VIRTUAL SCHOOL OF NATURAL SCIENCES, BIOMOO, OR ANY OTHER
 PARTICIPATING VOLUNTEER HAVE BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

 THE GLOBEWIDE NETWORK ACADEMY, THE VIRTUAL SCHOOL OF NATURAL SCIENCES, BIOMOO,
 AND ANY OTHER PARTICIPATING VOLUNTEER SPECIFICALLY DISCLAIM ANY WARRANTIES,
 INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY
 AND FITNESS FOR A PARTICULAR PURPOSE.  THE CLASS PROVIDED HEREUNDER IS ON AN
 "AS IS" BASIS, AND THERE IS NO OBLIGATION WHATSOEVER TO PROVIDE MAINTENANCEE,
 SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

GNA course catalog entry:

Biocomputing I: Sequence Analysis

Georg Fuellen (coordinator), M.Sc. (MIT, 1994),
Diplom-Informatiker (Saarbruecken, 1992).

For up-to-date information, and to obtain a list of
all collaborators, please use a www/hypertext browser
(e.g. Mosaic, Lynx) to visit
http://www.techfak.uni-bielefeld.de/techfak/persons/fuellen/BCChome.html
 or
http://www.mit.edu:8001/afs/athena/user/f/u/fuellen/News/Ga/REM/Gna/BCChome.html

Graduate students and students close to the completion of their
undergraduate studies shall be given a profound introduction into
biosequence analysis and comparison. Instructors shall guide them through
a peer-reviewed hypertext book, by means of weekly online discussion
sessions, supplemented by homework, personal advice, mailing list
discussions, and project work.

The core units shall cover Pairwise Alignment, Networking, Multiple 
Alignment, Mathematical Analysis of Sequence Data, Alignment and 
Phylogenetic Trees, and Pattern Matching on Biosequences. Units about Protein
Design, Ethics and Software Issues, shall provide basic introductions
into related areas.

Sponsors: VSNS, Research Center for Studies on Structure Formation
and Research Group Practical Informatics (University of Bielefeld)
Instructor's email address: (PLEASE VISIT OUR HOMEPAGE FIRST !)
vsns-bcd-admcoord@techfak.uni-bielefeld.de
Schedule:  Regular intervals throughout the week (to be announced)
~10 weeks, expected to start in May 1995.
Location: BioMOO (telnet bioinformatics.weizmann.ac.il 8888)
Level: late undergraduate (senior) or early graduate
Credits: None.
Language of Instruction: English
Status: teachers wanted, under construction (registration is scheduled
for early Spring 1995.)
Requirements: Technical: telnet, www/hypertext browser supporting
black&white graphics, and Forms. Academic: undergraduate level maths 
experience, computer science and/or molecular biology. More details will be
announced on our www/hypertext homepage. Some read-only tutorial
material (e.g. in chemistry, biochemistry) might be offered to
bring students to a common starting point.


--
kindest regards,
  georg
fuellen@dali.Mathematik.Uni-Bielefeld.DE
fuellen@MIT.EDU   fuellen@Techfak.Uni-Bielefeld.DE
   Dr Stephen R Covey, The 7 Habits of Highly Effective People, Habit #3:
   Put First Things First !


