DAS writeback

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DAS writeback presented in the DAS workshop 2011

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DAS writeback

  1. 1. DAS Writeback and its integration in Dasty2 as a proof of concept Gustavo Adolfo Salazar Orejuela Supervised by: Prof. Edwin Blake Cosupervised by: Dr Nicola Mulder DAS workshop - 2010
  2. 2. Outline <ul><li>Distributed Annotation System </li></ul><ul><li>Problem Definition </li></ul><ul><li>Proposed Solution </li></ul><ul><ul><li>Architecture </li></ul></ul><ul><ul><li>Protocol </li></ul></ul><ul><ul><li>Server </li></ul></ul><ul><ul><li>Client </li></ul></ul><ul><li>Future Work </li></ul>
  3. 3. DAS Distributed Annotation System
  4. 4. Problem Definition <ul><li>How the current DAS infrastructure can be extended in order to capture and use information provided for the users? </li></ul>
  5. 5. Proposed Solution DAS Writeback architecture
  6. 6. Proposed Solution Writeback protocol <ul><li>DAS 2.0 v.s. DAS1.53 Writeback </li></ul><ul><ul><li>New Format v.s. reuse DASGFF </li></ul></ul><ul><ul><li>New model v.s. reuse MyDAS model </li></ul></ul><ul><ul><li>Embedded Functions v.s. Uniform interface </li></ul></ul><ul><ul><li>Small v.s.medium size database schema </li></ul></ul>
  7. 7. Proposed Solution Server - MyDAS extension <ul><li>MyDAS </li></ul><ul><ul><li>Java DAS Servlet </li></ul></ul><ul><ul><li>Generic server. The user develop the data source in a free way as soon as he implements the right interface </li></ul></ul><ul><ul><li>Implements DAS 1.53 </li></ul></ul><ul><li>Extension </li></ul><ul><ul><li>Core extension for new commands </li></ul></ul><ul><ul><li>Implementation of a writeback data source </li></ul></ul><ul><ul><li>Database PostgreSQL </li></ul></ul><ul><ul><li>Basic Authentication </li></ul></ul>
  8. 8. Proposed Solution DAS clients
  9. 9. Proposed Solution Writeback client - Communication <ul><li>Proxy for the RESTful architecture </li></ul><ul><ul><li>DELETE </li></ul></ul><ul><ul><li>PUT </li></ul></ul><ul><ul><li>POST </li></ul></ul><ul><ul><li>GET </li></ul></ul><ul><li>Authentication with the server </li></ul><ul><li>JavaScript <=> PHP <=> J2EE </li></ul>
  10. 10. Proposed Solution Writeback client - Feature tabs <ul><li>Feature details </li></ul><ul><li>Edit Feature details </li></ul><ul><li>Delete Feature </li></ul><ul><li>Feature History </li></ul>
  11. 11. Proposed Solution Writeback client - Snapshot
  12. 12. Future work <ul><li>On progress </li></ul><ul><ul><li>Writing the paper. </li></ul></ul><ul><ul><li>MyDAS Writeback to 1.6 </li></ul></ul><ul><li>Outstanding: </li></ul><ul><ul><li>Non positional features </li></ul></ul><ul><ul><li>Dasty3 + Writeback to 1.6 </li></ul></ul><ul><li>Future </li></ul><ul><ul><li>Ratings for user and features </li></ul></ul><ul><ul><li>Implementation in other clients (Kariotype?) </li></ul></ul>
  13. 13. Acknowledgments <ul><li>Supervisors </li></ul><ul><ul><li>Professor Edwin Blake </li></ul></ul><ul><ul><li>Doctor Nicola Mulder </li></ul></ul><ul><li>University of Cape Town </li></ul><ul><ul><li>CBIO laboratory </li></ul></ul><ul><ul><li>Computer Science Department </li></ul></ul><ul><li>National Bioinformatics Network (South Africa) </li></ul><ul><li>EBI </li></ul><ul><ul><li>Henning Hermjakob </li></ul></ul><ul><ul><li>Philip Jones </li></ul></ul><ul><ul><li>Rafael Jimenez </li></ul></ul><ul><li>Writing editors </li></ul><ul><ul><li>Elizabeth Kelly </li></ul></ul><ul><ul><li>Alex Garcia </li></ul></ul><ul><li>All the people of the DAS email list </li></ul><ul><ul><li>Andy Jenkinson </li></ul></ul><ul><ul><li>Jonathan Warren </li></ul></ul><ul><ul><li>[email_address] </li></ul></ul><ul><ul><li>http://lists.open-bio. org/mailman/listinfo/das </li></ul></ul>
  14. 14. Questions??

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