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Dasty2, a web client for visualizing protein sequence features

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Dasty2 is a web client for visualizing protein sequence feature information using DAS protocol.

Dasty2 is a web client for visualizing protein sequence feature information using DAS protocol.

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  • 1. Dasty2 Omar Pera Background Dasty2 Features Advanced Search page Configuration system A web client for visualizing Demonstration protein sequence features Omar Pera Mira ECCB 2008 in Sardinia, Italy
  • 2. Outline of the presentation Dasty2 Background: DAS Omar Pera Dasty2 Background Features Dasty2 Advanced search page: MyDasty Features Advanced MyDasty configuration system Search page Acknowledgments Configuration system Demonstration Demonstration
  • 3. Background: DAS Dasty2 Distributed Annotation System. Omar Pera RESTful web service (XML data through HTTP Background requests) Dasty2 Uniform access to multiple repositories of biological Features data Advanced Search page Different biological data types: Configuration Genome system Protein sequence Demonstration Protein annotations .. Widely adopted system URL: http://biodas.org
  • 4. Background: DAS Dasty2 Omar Pera Background Dasty2 Features Advanced Search page Configuration system Demonstration The Distributed Annotation System, 2001 Dowell et al; BMC Ilustration of Andreas Kähäri Bioinformatics. 2001; 2: 7. Published online 2001 October 10.
  • 5. Dasty2 Dasty2 is a web client for visualizing protein sequence Dasty2 feature information using DAS. Omar Pera Background Lightweight Dasty2 Highly customizable Features Makes use of AJAX (asynchronous loading + local Advanced Search page caching) Configuration system Easy to integrate in other systems Demonstration Extensible Open Source: http://sourceforge.net/projects/dasty/ URL : http://www.ebi.ac.uk/dasty
  • 6. Dasty2 Dasty2 Omar Pera Background Dasty2 Features Advanced Search page Configuration system Demonstration
  • 7. Dasty2 Dasty2 Omar Pera Background Dasty2 Features Advanced Search page Configuration system Demonstration
  • 8. Dasty2 Dasty2 Omar Pera Background Dasty2 Features Advanced Search page Configuration system Demonstration
  • 9. Dasty2 Dasty2 Omar Pera Background Dasty2 Features Advanced Search page Configuration system Demonstration
  • 10. Dasty2 Dasty2 Omar Pera Background Dasty2 Features Advanced Search page Configuration system Demonstration
  • 11. Dasty2 Dasty2 Omar Pera Background Dasty2 Features Advanced Search page Configuration system Demonstration
  • 12. Features Protein sequence visualization Dasty2 Positional features Omar Pera Background Dasty2 Features Protein sequence visualization 3D protein structure viewer DAS ontology integration Non Positional features Advanced Search page Configuration system Demonstration
  • 13. Features 3D protein structure viewer Dasty2 Omar Pera Background Annotation on 3D protein space: Dasty2 Features Highlight annotation on the 3D Protein sequence structure visualization 3D protein structure viewer Select 3D regions and highlight DAS ontology integration correspondence in the protein Advanced Search page 3D structure rotation, zoom, etc.. Configuration system Demonstration
  • 14. Features DAS ontology integration for data manipulation Dasty2 In order to classify protein annotations, a protein Omar Pera feature ontology is avaliable in DAS. Background Dasty2 Features Protein sequence visualization 3D protein structure viewer DAS ontology integration Advanced Search page Configuration system Demonstration
  • 15. Features DAS ontology integration for data manipulation Dasty2 In order to classify protein annotations, a protein Omar Pera feature ontology is avaliable in DAS. Background Dasty2 integrates DAS ontology information found in Dasty2 the current protein to filter annotations by: Features Protein sequence Protein feature types visualization 3D protein structure Evidence viewer DAS ontology integration Advanced Search page Configuration system Demonstration
  • 16. Advanced Search page: MyDasty Dasty2 MyDasty is an extension of the search page that makes Omar Pera Dasty2 a more configurable and powerful application. Background Dasty2 Features Advanced Search page Das sources selection Filtering annotations Mapping protein accessions from other databases Configuration system Demonstration
  • 17. MyDasty Dasty2 Let users have more control over the search before Omar Pera the client starts. Background Give the option to save and restore your Dasty2 configuration. Features Easy to extend with other ’plugins’ Advanced Search page Independent from Dasty2 Das sources selection Filtering annotations Developed recently, not yet in production Mapping protein accessions from other databases Configuration system Demonstration
  • 18. Features Das sources selection Full control of the DAS sources Dasty2 retrieves protein Dasty2 annotations from using DAS registry: Omar Pera Background Select individually which DAS servers are queried for Dasty2 features. Features Filter the servers by label in order to make easier the Advanced selection. Search page Das sources selection Insert test or private DAS sources to display on Dasty2. Filtering annotations Mapping protein accessions from Sort the selected DAS sources: Dasty2 graphic. other databases Configuration system Demonstration
  • 19. Features Das sources selection Dasty2 Omar Pera Background Dasty2 Features Advanced Search page Das sources selection Filtering annotations Mapping protein accessions from other databases Configuration system Demonstration
  • 20. Features Filtering annotations using the DAS ontology Pre-configure Dasty2 to just display annotations of a Dasty2 certain type or category. Omar Pera Background Dasty2 Features Advanced Search page Das sources selection Filtering annotations Mapping protein accessions from other databases Configuration system Demonstration
  • 21. Features Mapping protein accessions from other databases Protein Identifier Cross-Reference service ( PICR ) is a Dasty2 tool capable of mapping protein identifiers to a large list of Omar Pera databases. Background Dasty2 Features MyDasty uses PICR to: Advanced Search page Map from different source databases such as IPI, Das sources selection Ensembl, TrEMBL or PIR to Uniprot protein accession Filtering annotations Mapping protein number, extending the possibilities of Dasty2 accessions from other databases Configuration system Demonstration
  • 22. Features Mapping protein accessions from other databases Protein Identifier Cross-Reference service ( PICR ) is a Dasty2 tool capable of mapping protein identifiers to a large list of Omar Pera databases. Background Dasty2 Features MyDasty uses PICR to: Advanced Search page Map from different source databases such as IPI, Das sources selection Ensembl, TrEMBL or PIR to Uniprot protein accession Filtering annotations Mapping protein number, extending the possibilities of Dasty2 accessions from other databases Configuration system Demonstration
  • 23. Configuration system We have to consider two types of users on MyDasty: Dasty2 Omar Pera Anonymous: Users that just want to customize their current Background search. No need to store the config for future Dasty2 uses. Features Registered: They are users who want to save their Advanced configuration on the server. It means that all Search page Configuration the parameters configured on myDasty could system be restored in the future. Demonstration
  • 24. Registered users OpenID Dasty2 It is a shared identity service that makes use of a single Omar Pera digital identity, eliminating Background the need for a different user Dasty2 name and password for each Features site. Advanced Search page Configuration system Demonstration
  • 25. Registered users Options Dasty2 History of the previous proteins inserted on Omar Pera myDasty. Background Dasty2 Features Advanced Search page Configuration system Demonstration
  • 26. Registered users Options Dasty2 History of the previous proteins inserted on myDasty. Omar Pera Save multiple configurations with a specific name. Background Dasty2 Features Advanced Search page Configuration system Demonstration
  • 27. Registered users Options Dasty2 History of the previous proteins inserted on myDasty. Omar Pera Save multiple configurations with a specific name. Background Dasty2 Features Advanced Search page Configuration system Demonstration
  • 28. Registered users Options Dasty2 History of the previous proteins inserted on myDasty. Omar Pera Save multiple configurations of myDasty with a specific Background name. Dasty2 Update, delete, change name or create new Features configurations. Advanced Search page Configuration system Demonstration
  • 29. Acknowledgments Dasty2 Funding and collaborations Omar Pera Supervision Background Henning Hermjakob, EMBL-EBI, UK Dasty2 Features Development Advanced Rafael C. Jimenez, Search page EMBL-EBI, UK Configuration NBN central node, South Africa system CiPF, Spain Participation and collaboration Antony Quinn, Demonstration EMBL-EBI, UK Phil Jones, EMBL-EBI, UK Alberto Labarga, Development EMBL-EBI, UK Lennart Martens, EMBL-EBI, UK Nisha Vinod, Rafael C. Jimenez, EMBL-EBI, UK Florian Reisinger, EMBL-EBI, U EMBL-EBI, UK Dan Jacobson, NBN central node, South Africa NBN central node, CiPF, Spain Eugene Kulesha, South Africa Antony Quinn, EMBL-EBI, UK EMBL-EBI, UK Antony Quinn, Andreas Kahari, Andreas Prlic, EMBL-EBI, UK EMBL-EBI, UK Sanger Institute, UK
  • 30. Demonstration Dasty2 Demonstration Omar Pera Background Dasty2 Features Advanced Search page Configuration system Demonstration