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.
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 ---------------|
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