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Share your opinion - Sight feedback form available, check boxes only
by Audrius Meškauskas - Nov 1st 2004 06:30:21
Sight is getting more and more complex. It is possible to
concentrate further development in many possible directions. Where to focus
the attention? You can help us by telling your opinion using this feedback form. The
form contains check boxes only and will not take much your time.
--
Audrius Meskauskas
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Sight 3.0.0 alpha released (WSDL, loops, etc)
by Audrius Meskauskas - Sep 11th 2004 16:08:09
Sight 3.0.0 alpha is developed by Audrius Meškauskas as a
subsequent stage of the GPL-based Sight project, initially
started in Ulm
university. This release has several important new features:
Sight now supports workflows, containing loops
and confluences. This allows to implement much
more variable strategies of the bioinformatical research.
Built – in Smith and Waterman search
allows searching the local database for the related
sequences.
Cross platform implementation of WSDL
compatible protocol allows to integrate web services
using this way of communication.
The whole Sight workflow now can be converted into a
single Sight agent. Such combined agents
are valuable not just as an “elementary units”
in more complicated workflows, but also as a simply
usable modules for java programmer.
Sight now has agents for reading and writing in SwissProt
and FASTA formats an can be used as a system to search or
classify data in flat files having these formats.
Sight provides a “mini environment” to test and
create data filters, based on java regular expressions.
Improved user environment (for example, possibility to
copy/paste a part of workflow) makes creating of
workflows easier.
XML agent generator supports namespaces.
Table agent generator supports turned tables and some
cases when the response must be composed from the several
tables in the document.
Manual landmark marking agent generator now uses regular
expressions to specify landmarks.
Sight now can work with workflows where the final result
is a graph rather than a table. The annotation event
listener accepts registers events when two named nodes
must be connected by the named link. Generated graphs can
be viewed using CytoScape (see http://www.cytoscape.org/).
The new version has a large number of the other small
improvements and fixed bugs.
This alpha-pre release is still not properly documented. While
the user manual is in preparation, we suggest to read the button
tool tips and try to understand the general logic of the program.
Audrius
Meškauskas will also be glad to answer all questions.
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