Sight: Web robot generator - Summary

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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

Public areas This project has many places for you to explore and participate. The icons displayed below are also available at the top of the page for easy navigation.  Project homepage This home page points to the official page for this project, which may or may not be hosted at Bioinformatics.org.  Public forums There are 6 messages in 2 forums.  Project manager There are 0 open, public tasks, 0 total.  Support tickets There are 0 open tickets, 0 total.  Mailing lists There are 2 public mailing lists.  Public surveys There are 0 active surveys. SCM repository The SCM repository is a place for this project to store its source code. Members have access to change this master repository, while anonymous users may browse the most recent development version of this project. Instructions Download directory Projects may choose to have files other than their main releases available via this directory.

Members Project admins: Audrius Me?kauskas Members: 1 [View all members] Downloads 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. [View all files] Latest announcements Submit Archive Subscribe 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. [1] http://bioinformatics.org/project/?group_id=148 [2] http://bioinformatics.org/project/?group_id=210 Submit Archive Subscribe