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Title: Dasty2: A web client for Visualizing protein sequence features …

Title: Dasty2: A web client for Visualizing protein sequence features
Author: Rafael C. Jimenez

Published in: Business, Technology

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  • 1. A web client for visualizing protein sequence features Rafael C. Jimenez BOSC 2007 at ISMB 2007 in Vienna, Austria
  • 2. Outline of this presentation
    • DAS
    • Dasty2
    • Work in progress: Dasty2 extensions
    • DAS and Dasty2 at the ISMB-SIG
    • Acknowledgments
    • Dasty2 examples
  • 3. DAS
    • Distributed Annotation System.
    • RESTful web service (XML data through HTTP requests)
    • Uniform access to multiple repositories of biological data.
    • Repositories distributed in different geographical locations.
    • Different biological data types:
    • - Genome
    • - Protein sequence
    • - Protein structure
    • - …
    • System widely adopted.
    • Requires visual clients (connect + merge + display).
    • URL: http://biodas.org
  • 4. DAS The Distributed Annotation System, 2001 Dowell et al; BMC Bioinformatics. 2001; 2: 7. Published online 2001 October 10. illustration
  • 5. Dasty2
    • It is an Ajax web-based protein DAS client (asynchronous loading + local caching).
    • Lighweight.
    • Highly customizable
    • - User
    • - Developer
    • Easy to integrate in other systems.
    • Extensible.
    • URL: http://www.ebi.ac.uk/dasty/
  • 6. Dasty2 Query page Request module Annotation servers (features.xml) Diplaying page Reference server (seqeunce.xml) Visualization module
  • 7. Dasty2 extensions Extensions aim to enrich Dasty2 by: - Visualizing more data types provided by DAS. - Providing extra functionality to domain experts. Extensions: - Integration server - Three dimensional protein structure viewer - Genome viewer - Display multiple aligment results - Visual ontology query tool - Advance search web page
  • 8. More about DAS and Dasty2 AFP-Biosapiens SIG meeting Dasty2 (posters session) Today, Thursday from 12:00 to 2:00 OntoDas by Kieran O'Neill (talk) Tomorrow, Friday from 09:50 to 10:10 DAS by Andreas Prlic (talk) Tomorrow, Friday from 16:50 to 17:10 Ontology SIG meeting OntoDas by Kieran O'Neill (talk) Tomorrow, Friday from X to Y
  • 9. Acknowledgments Supervision - Henning Hermjakob , EMBL-EBI, UK Development - Rafael C. Jimenez , EMBL-EBI, UK NBN central node, South Africa - Antony Quinn , EMBL-EBI, UK Participation and collaboration - Alberto Labarga , EMBL-EBI, UK - Andreas Prlic , Wellcome Trust Sanger Institute, UK - Eugene Kulesha , EMBL-EBI, UK - Nisha Vinod , EMBL-EBI, UK - Philip Jones , EMBL-EBI, UK - Andreas Kahari , EMBL-EBI, UK - Alexander Garcia , NBN central node, South Africa - Kieran O'Neill , NBN central node, South Africa - Dan Jacobson , NBN central node, South Africa Funding and collaborations Ministerio de Educacion y Ciencia BioSapiens Network of Excellence European Commission (FP6 Programme) Proteomics Services EBI-EMBL National Bioinformatics Network of South Africa
  • 10. Dasty2 examples
    • Local installation - Remote DAS http://localhost/ebi2/dasty2dev/display.html?q=P05067&label=BioSapiens&t=3
    • Local installation - Local XML http://localhost/ebi2/dasty2dev_local/display.html?q=P05067&label=BioSapiens&t=3
    • Remote installation (EBI) - Remote DAS
    • http://www.ebi.ac.uk/dasty/display.html?q=P05067&label=BIOSAPIENS&t=3
    • Remote installation (NBN) - Using OntoDas http://ontodas.nbn.ac.za/static/dasty.html?q=P05067&label=BioSapiens&t=3