Bioinformatics.org
[Trainer-Lead Program in Bioinformatics]
Not logged in

Bioinformatics.org
Membership (36908+) Group hosting [?]

Careers
About bioinformatics
Bioinformatics training
Bioinformatics jobs

Research
All information groups
Online databases Online analysis tools Online education tools More tools

Development
All software groups
FTP repository
SVN & CVS repositories [?]
Mailing lists

Forums
News & Commentary
Jobs Forum
(Career Center)

Sight: Web robot generator - News

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

Submit Archive Subscribe

 

Acknowledgments

We wish to thank the following for their support:

[Scalable Informatics]
[Become a sponsor]
Copyright © 2016 · Scilico, LLC