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  • Sight: Web robot generator - Summary

    All categories :: bioinformatics software development :: Sight: Web robot generator

    Sight, a java-based package that provides a user-friendly interface to create and connect agents for automatic genomic data mining for individual purposes. No programming skills are required, but very strong support for programmers is implemented.

    License: GNU General Public License

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    Project admins: [Photo] Audrius Me?kauskas

    Members: 1 [View all members]
    Module name: Sight cross platform
    Latest release is 3.2.0 beta
    View: [Release Notes & Changelog]
    Download: [jar]
    Module name: Sight Windows
    No files in the latest version: 3.1.0 alpha.
    Module name: Sight Linux
    No files in the latest version: 3.1.0 alpha.
    Module name: Cross platform service packs
    No files in the latest version: 3.1.0 alpha.
    Module name: Application examples
    No files in the latest version: 3.1.0 alpha.

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    Latest announcements
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    Sight 3.1.0a released
    Submitted by Audrius Me?kauskas; posted on Tuesday, October 26, 2004


    Sight 3.1.0.a released, adding autoupdate support and upgrading WSDL to 1.1.
    Sight 3.0.0 alpha
    Submitted by Audrius Me?kauskas; posted on Saturday, September 11, 2004


    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.
    Scientific article about "Sight" is in press.
    Submitted by Audrius Me?kauskas; posted on Wednesday, February 11, 2004


    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".
    lication examples available
    Submitted by Audrius Me?kauskas; posted on Thursday, November 13, 2003


    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.
    DAS-based web robot generator is implemented
    Submitted by Audrius Me?kauskas; posted on Wednesday, March 19, 2003


    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.
    Sight integrates BioQuery
    Submitted by Audrius Me?kauskas; posted on Thursday, February 20, 2003


    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.


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