history, and thoughts on the future of biogophers (RE: What is a ...)

Reinhard Doelz doelz at comp.bioz.unibas.ch
Tue Jun 22 02:12:57 EST 1993



=== history : GOPHER in Biology ===

My first reference to a 'GOPHER' came from Robert Harper, the 
famous Bionaut from the CSC Helsinki. He's very ambitious and 
succeeds to report new developments of the networking people... 

Message-ID: <199202131548.AA01763 at convex.csc.fi>
Date: 13 Feb 92 17:48:32 GMT
>                                 No 22
>   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>                        BIO-NAUT NEWSLETTER 12-2-92
>                       << EDITED BY ROBERT HARPER >>
>    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>
>                         GO FOR IT WITH GOPHER

(Available via gopher from: )
Name=BioBit No22 (Go for it with Gopher)
Type=0
Port=70
Path=R0-15627-/IUBio-Software+Data/help/biobits/biobit.gopher.text
Host=ftp.bio.indiana.edu

Only 4 days later, the following surfaced the networks: 
Message-ID: <1992Feb17.023313.4530 at bronze.ucs.indiana.edu>
Date: Mon, 17 Feb 92 02:33:13 GMT

>This rather long note is in response to questions about what to make
>of Internet Gopher, WAIS and other Internet information searching
>methods, and specifically how does this relate to Genbank keyword
>searching and entry fetching, as compared with the IRX service at
>genbank.bio.net, and perhaps to e-mail services.

(Full text on:)
Name=Don Gilbert`s original gopher port to biology
Type=0
Port=70
Path=0/About Gopher, and this bioftp site/Don Gilbert`s original gopher port to biology
Host=biox.embnet.unibas.ch

The next reference came from the most daring Computer Biologist at the 
time who had the nerve to try it out: 
Message-ID: <1992Feb24.235003.22307 at cica.indiana.edu>
Date: Mon, 24 Feb 92 23:50:03 GMT

and it was Don Gilbert saying, 

>I've about finished setting up an Internet Gopher server for
>biology data at ftp.bio.indiana.edu. It seems to be working well
>and biologists look like they are taking to it rapidly and
>easily -- I would say it has some of the good features of both
>ftp and wais, but is a good bit easier to learn.

(full text on GOPHER from: )
Name=Don Gilbert`s indexing port to biology
Type=0
Port=70
Path=0/About Gopher, and this bioftp site/Don Gilbert`s indexing port to biology
Host=biox.embnet.unibas.ch


I joined the game February 27, announcing the european leg of the 
WAIS indexing stuff as implemented first by Don Gilbert, and announced
a mailing list in 
Message-ID: <1992Feb27.221816.11563 at urz.unibas.ch>
Date: 27 Feb 92 21:18:16 GMT
and used the word 'biogopher' as mailing list name. (Thanks Don for pointing
me at it - I almost forgot). Unfortunately, the purpose of the mailing list was 
developmental, and it died because in the beginning the biogophers knew each 
others quite well. Tim Littlejohn suggested a revival of this list recently.



=== Evaluation of GOPHER as a tool ===

If asked what the benefit of these biogophers is, ask Dan or Don or 
anyone on the net who made a successful query. There are several points 
which are partially intrinsic to GOPHER and partially specific to biology: 
(totally unsorted, jumping off my head). 

	o it is all public domain: You get what you paid for.
	+ many people use it. Good chance to get patches released.
	- documentation is hairy. Need some experience for providers.
	o was never meant to be a world-wide system.
	- gopher+ future is unclear, as is U Minnesota's commitment to the 
		gopher theam whether to support the world for free. 
	o underlying search engine is WAIS
	- WAIS went commercial recently. Usefulness of FREEWais unclear.
	- WAIS is full-text. Entry-specific search would be better.
	- special indices are huge. Incompatible with GCG Blast Pir other.
	+ Browsing possible without cost.
	- As all is voluntarily, low reliability on quality. 
	+ interfaces on all platforms. 
	+ does not need Xwindows 
	+ may use XWindows if available
	+ may use PC/Mac if available
	+ Client support for VMS is available 
	- VMS server is rarely used 
	- uses networks extensively. Who pays? 
	- needs excellent networks (name server support)

All in all, we are glad to have it but it isn't the last kick. Question 
being, would you like to pay for 'THE' optimal interface, and would all 
the service providers like to pay in order to allow always for free ser-
vices? I doubt it. I would like to see interfaces coming up which allow
for a moderate usage, but truncate after a while if abusage is suspected.
E.g., I noticed that some sites use my GOPHER as retrieval of thousands (!) 
of entries. Obviously, someone has written a procedure to use some sort
of input file to retrieve all entries en block. That is nice for 10 hits, 
but garty and network-asocial for thousands. 


One last statement: Thanks to Dan Jacobson, there is now a browsing 
of gopherspace possible explicitly for Biology (BOING). 


=== How to find GOPHERs in Biology ===

In Europe, we have tried to set up a network of Gophers in the framework 
of the European Molecular Biology Network (EMBnet). These 
nodes are committed to offer some standardized tree look-and-feel, 
and deliver Biocomputing services to european countries. Ask your 
nearest EMBnet node how to set up a GOPHER, or how to maintain a
client to the national EMBnet Gopher. 

If you go for the European entry point for subjects, 

Name=Subject Tree
Type=1
Port=70
Path=1/Subject Tree
Host=sunic.sunet.se

or its US counterpart, 

Name=Information by Subject Area (from RiceInfo, Rice Univ.)
Type=1
Port=70
Path=1/Subject
Host=chico.rice.edu

you will find many, many, many hosts in all sort of different areas. 
E.g., on gopher.embnet.unibas.ch I maintain a subject tree for biology, 
and use this as link service. There is one item there which is called
Name=this file is the Index
Type=0
Port=70
Path=0/Information Servers in biology (Gopher based)/this file is the Index
Host=yeti.embnet.unibas.ch

and this is a link list of biogophers. 


Regards
Reinhard 


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