Under Windows environment, this recent versions
need 1.4 java runtime environment that must be accessible by the path without
spaces. For instance, C:\Program files\java is not an appropriate location,
despite C:\Programme is ok. This minor bug will be fixed in a subsequent
The Software Patents Directive, as approved by the European Council of Ministers, would codify US-style Software Patents in the European Union. If that happens, software developers will no longer own what they write and can be sued for selling or distributing their own software. This would not only endanger your job, but the entire European software sector. Patents on pure logic would even restrict the freedom of publication. ... read more
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 feedback form at http://jsight.sourceforge.net/feedback.htm. The form contains check boxes only and will not take much your time.
NEW: Sight 3.0.0 alpha released!
Sight 3.0.0 alpha is developed by Audrius Mekauskas 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 Mekauskas will also be glad to answer all questions.... read more
Scientific article (Sight: automating genomic data-mining without programming skills. A.Meskauskas, F.Lehmann-Horn, K.Jurkat-Rott) has just been accepted by independent referees and will appear in one of the subsequent releases of "Bioinformatics".
Despite the previous Sight versions were able to generate cross-platform java applications, they were later only modifyable by a programmer. Since 2.1.2 SP 1 it is possible to save the assembled web agent workflows in a team files (.tjar), alowing later modifications and subsequent code generation. This simple improvement allows us to suggest various examples of the application workflows, leading to easier understanding that can be done with this program.
In the recent Sight version, the distributed annotation system (DAS) support was added. DAS is a popular bioinformatical standard, based on http-like server requests and XML-based server responses. DAS is currently supported on a large number of bioinformatical servers (see www.biodas.org). DAS is mainly used to read the DNA sequences and annotated features of the sequenced genomes. Sight 2.1.2 can now work as DAS client and may be even tried as the DAS server.
Sight is a code generator set to create a user-defined system of web robots, realising arbitrary workflow. This task frequent in bioinformatics, but may also arise in other areas.
Sight 2.1.1 has improved xml transform wizard, improved Weka and SSH plug-ins and BioQuery plug-in. Linux, Windows and cross plafrom installers are available.