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Sight: Web robot generator - News
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Latest announcements
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Sight 3.1.0.a released, adding autoupdate support and upgrading WSDL to 1.1.
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Sight 3.0.0 alpha is developed by Audrius Me?kauskas as a subsequent stage of the GPL-based Sight project, initially started in Ulm university. This release has many important new features: loops, confluences, WSDL support, built-in Smith and Waterman search and so on (see project web page for details).
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 Me?kauskas will also be glad to answer all questions.
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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".
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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.
This release includes sample applications (web robot teams). You need at least version 2.1.2 service pack 1 to open them.
Genome_walker.tjar performs analysis of the given DNA fragment or fragments, representing genome fragment or small (bacterial or viral) genome.
Protein_explorer.tjar performs various analysis on the protein sequence, corresponding the given NCBI accession number. Can take some RNA sequences if the corresponding XML entry contains protein translation.
Specific_range.tjar scans the 200 amino acids upstream the third transmembrane helix for PROSITE hits and NCBI conservative domains. The imput is the list of NCBI accession numbers to the protein sequences. As this is a public example, we used the simple and fast-responding servers.
Blast_blast_blast.tjar can re-submit the received BLAST hits to BLAST similarity search again. The iteration is repeated 3 times. The team investigates problems and possibilites for this way of finding the similarity between proteins, also can be useful in understanding BLAST limitations.
In future, we plan to release more examples. We would be glad to accept and display the user-created applications.
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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 [1,2]). DAS is mainly used to read the DNA sequences and annotated features of the sequenced genomes. Sight 2.1.2 can generate web robots that work as DAS clients.
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BioQuery [1] is a specialised web robot for quering biomedical databases. Sight [2] generates a web robot applications realising a user-defined tree-like workflow between web robots and local applications. Despite Sight has its own code generators for creating new web robots, it is an advantage to integrate some specialised human-written modules. We wrote a small, simple adapter that allows BioQuery robot to work in Sight workflow. This new plug-in is available since the Sight 2.1.1.
[1] http://bioinformatics.org/project/?group_id=148
[2] http://bioinformatics.org/project/?group_id=210
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