IUBio GIL .. BIOSCI/Bionet News .. Biosequences .. Software .. FTP


Reinhard Doelz doelz at comp.bioz.unibas.ch
Fri Sep 16 05:10:57 EST 1994

Przemko (przemko at reks.uia.ac.be) wrote:
: When I use Mosaic to access various databases to do searches, 
: sequence comparisons etc. I discovered a problem. It seems that I cannot 
: submit actual sequences. See, I am not going to retype 2000 bases, or to
: submit a Fasta formatted multiple alignement file for a 
: domain search, Sequence Logos etc.
: Any idea how I could place a file in the search quesry of Mosaic?
: Even cut/paste does not work if a query is too large...

Short answer: No way, cut+paste is the only method. 

Long answer:  

Mosaic is using the http - protocol, which does specify a language 
used by a client (==you) to a server (==the provider) in order to 
submit a request for a document, link, or query. These 'queries' have 
to be in a given format, and this is a problem for file transmissions; 
as the format definition (computer colleagues know this as MIME definition)
is cruical for success. Obviously, the different formats applied to 
biological sequence data would need to be known to Mosaic as the client.
Other distinct areas or disciplines will need other formats, and, in the
end the general-purpose nature of http would be endangered. 

Secondly, http is _synchronous_, i.e. you must wait for the answer while 
the computation runs at the provider. This implies severe problems at 
the client if many windows hold connections all the time. For searches 
in databases, the term 'computation' were more appropriate, as the 
original http paradigm of a query was based on Z39.50 keyword lookups 
(known from the WAIS implementation). Computations, however, need to be 

Lastly, all the license, resource-balancing, security, fault-tolerance 
etc. issues apply (not to forget accounting :-( ). http can be tweaked 
into some of the possible solutions, but is not made for these purposes.

We are currently developing the HASSLE receptors and -reflectors for the 
http protocol, in order to get our HASSLE system integrated into WWW. 
It might take a while, though, as software still has to be finalized. 
HASSLE is already available now, integrated in software packages (e.g., 
the GCG (GCG Inc., Madison) package),  on some EMBnet nodes. 


Note that  the software  mentioned  resembles  Computer  Program(s)  which 
require a license in order to be run unless stated otherwise in  a  state-
ment  codistributed with the software. The use of the program(s) was  men-
tioned  within  a specific problem or example and must not be used to con-
clude that other  software products cannot possibly do a similar job. 

 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 ---------------|
<a href=http://beta.embnet.unibas.ch/>EMBnet Switzerland:info at ch.embnet.org</a> 

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