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A web client for visualizing protein sequence features Rafael C. Jimenez BOSC 2007 at ISMB 2007 in Vienna, Austria
Outline of this presentation <ul><li>DAS </li></ul><ul><li>Dasty2 </li></ul><ul><li>Work in progress: Dasty2 extensions </...
DAS <ul><li>Distributed Annotation System. </li></ul><ul><li>RESTful web service (XML data through HTTP requests) </li></u...
DAS The Distributed Annotation System, 2001 Dowell et al; BMC Bioinformatics. 2001; 2: 7. Published online 2001 October 10...
Dasty2 <ul><li>It is an Ajax web-based protein DAS client  (asynchronous loading  + local caching). </li></ul><ul><li>Ligh...
Dasty2 Query page Request module Annotation servers  (features.xml) Diplaying page Reference server  (seqeunce.xml) Visual...
Dasty2 extensions Extensions aim to enrich Dasty2 by: - Visualizing more data types provided by DAS. - Providing extra fun...
More about DAS and Dasty2 AFP-Biosapiens SIG meeting Dasty2 (posters session) Today, Thursday from 12:00 to 2:00 OntoDas b...
Acknowledgments Supervision - Henning Hermjakob , EMBL-EBI, UK   Development - Rafael C. Jimenez , EMBL-EBI, UK NBN centra...
Dasty2 examples <ul><li>Local installation - Remote DAS   http://localhost/ebi2/dasty2dev/display.html?q=P05067&label=BioS...
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Title: Dasty2: A web client for Visualizing protein sequence features
Author: Rafael C. Jimenez

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  1. 1. A web client for visualizing protein sequence features Rafael C. Jimenez BOSC 2007 at ISMB 2007 in Vienna, Austria
  2. 2. Outline of this presentation <ul><li>DAS </li></ul><ul><li>Dasty2 </li></ul><ul><li>Work in progress: Dasty2 extensions </li></ul><ul><li>DAS and Dasty2 at the ISMB-SIG </li></ul><ul><li>Acknowledgments </li></ul><ul><li>Dasty2 examples </li></ul>
  3. 3. DAS <ul><li>Distributed Annotation System. </li></ul><ul><li>RESTful web service (XML data through HTTP requests) </li></ul><ul><li>Uniform access to multiple repositories of biological data. </li></ul><ul><li>Repositories distributed in different geographical locations. </li></ul><ul><li>Different biological data types: </li></ul><ul><li>- Genome </li></ul><ul><li>- Protein sequence </li></ul><ul><li>- Protein structure </li></ul><ul><li>- … </li></ul><ul><li>System widely adopted. </li></ul><ul><li>Requires visual clients (connect + merge + display). </li></ul><ul><li>URL: http://biodas.org </li></ul>
  4. 4. DAS The Distributed Annotation System, 2001 Dowell et al; BMC Bioinformatics. 2001; 2: 7. Published online 2001 October 10. illustration
  5. 5. Dasty2 <ul><li>It is an Ajax web-based protein DAS client (asynchronous loading + local caching). </li></ul><ul><li>Lighweight. </li></ul><ul><li>Highly customizable </li></ul><ul><li>- User </li></ul><ul><li>- Developer </li></ul><ul><li>Easy to integrate in other systems. </li></ul><ul><li>Extensible. </li></ul><ul><li>URL: http://www.ebi.ac.uk/dasty/ </li></ul>
  6. 6. Dasty2 Query page Request module Annotation servers (features.xml) Diplaying page Reference server (seqeunce.xml) Visualization module
  7. 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. 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. 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. 10. Dasty2 examples <ul><li>Local installation - Remote DAS http://localhost/ebi2/dasty2dev/display.html?q=P05067&label=BioSapiens&t=3 </li></ul><ul><li>Local installation - Local XML http://localhost/ebi2/dasty2dev_local/display.html?q=P05067&label=BioSapiens&t=3 </li></ul><ul><li>Remote installation (EBI) - Remote DAS </li></ul><ul><li>http://www.ebi.ac.uk/dasty/display.html?q=P05067&label=BIOSAPIENS&t=3 </li></ul><ul><li>Remote installation (NBN) - Using OntoDas http://ontodas.nbn.ac.za/static/dasty.html?q=P05067&label=BioSapiens&t=3 </li></ul>
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    Nov. 6, 2008

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

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