an EMBL gopher

Reinhard Doelz doelz at comp.bioz.unibas.ch
Sun Mar 12 03:59:04 EST 1995

G. Giacomo Consalez (consaleg at dibit.hsr.it) wrote:
: I have been looking for a functioning EMBL gopher server to retrieve
: genembl and genpept entries, just like I regularly do for genbank,
: swissprot and PIR entries. None seems to be running. A www server would be
: fine, although gopher products are much faster.

To my knowledge, we run the only database gopher on EMBL and EMBL updates 
world-wide. There are on average more than 300 requests served per day.
Peak requests are more than 1200 daily which is due to some unfortunate 
ambition to run automaitc scripts.  

There are two issues to be kept in mind.
	(1) The server runs on an Indigo3000, which is the same machine 
            which we introduced the service on in 1992. This machine 
            runs brilliantly but deserves a major CPU and memory upgrade 
            which is unfortunately unrealistic for such a service. 
            Updating GOPHER indices is a pretty resource-consuming step. 
            We currently need more than an hour to create the waisindex.
            If you apprach the server at that time you will get rejected.
            Depending on load, it can take up to a minute if you do get 
            a result in peak hours. 

        (2) WAIS-indexing is a full-text search. This means that a full 
            text is analyzed for keywords. The more keywords there are 
            the slower WAIS will become. Worse, it will not allow searches
            for trivial words ('protein', 'mrna') as it has a built-in 
            limitation to not incorporate words occuring more than a given

: Anybody with a good suggestion?

Use the WWW-based SRS browser from Thure Etzold; on many EMBnet nodes, 
including the one in Bari, you'll find local versions also. 
http://www.embl-heidelberg.de/srs/status.html is the overview on the 
available SRS servers on the network. 

: Thanks.

Question for the community: How long will this service need to run? 
Despite the disk space resources the machine which it is running on 
has been frozen in its OS. The code has been modified to an extend which 
makes it highly questionable whether it will ever run on a more advanced
OS version. This implies that, if the box dies, the service will die as 
well with short notice. Would you bother? 

Reinhard Doelz
EMBnet Switzerland
 R.Doelz         Klingelbergstr.70| Tel. x41 61 267 2247  Fax x41 61 267 2078|
 Biocomputing        CH 4056 Basel| electronic Mail    doelz at ubaclu.unibas.ch|
 Biozentrum der Universitaet Basel|-------------- Switzerland ---------------|
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