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Group Meeting Vamsas Project Final


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Group Meeting Vamsas Project Final

  1. 1. VAMSAS Project September 1rt, 2005 – February 2006 Pierre Marguerite
  2. 2. What is VAMSAS? <ul><li>Open framework that facilitates the interoperation of advanced tools for phylogenetics, sequence analysis, and structural bioinformatics, by providing a common model for bioinformatic data exchange, web service discovery and interaction. </li></ul>
  3. 3. <ul><li>Bringing three programs together… </li></ul>The VAMSAS Framework Visual Analysis of Molecular Sequences, Alignments and Structures Jalview Alignment Visualization Sequence Analysis ( University of Dundee Geoff Barton & David Martin Jim Procter, Andrew Waterhouse ) TOPAli DNA Recombination Phylogenetic Analysis ( Biomathematics and Statistics Scotland (BioSS) At Scottish Crop Research Institute (SCRI) Frank Wright & David Marshall Iain Milne ) [email_address] Molecular Graphics Conformation Analysis Reaction Diagrams (Tom Oldfield & Kim Henrick Pierre Marguerite ) VAMSAS
  4. 5. The VAMSAS Document <ul><li>XML model for core biological data types and annotation </li></ul><ul><ul><li>Database-like primary keys </li></ul></ul><ul><li>Provenance for primary and derived data </li></ul><ul><ul><li>What was done and when </li></ul></ul><ul><li>References for primary data </li></ul><ul><ul><li>Sequence IDs </li></ul></ul><ul><ul><li>Database cross references </li></ul></ul><ul><li>Data storage for each VAMSAS application </li></ul>BIOLOGICAL SEQUENCE AND ANALYSIS DATA JALVIEW DATA ASTEXVIEWER DATA TOPALI DATA References Provenance
  5. 6. VAMSAS Applications <ul><li>VAMSAS Apps have three main functions: </li></ul><ul><li>Data Import </li></ul><ul><ul><li>Translate data into VAMSAS XML </li></ul></ul><ul><li>Data Analysis </li></ul><ul><ul><li>Extend core data set </li></ul></ul><ul><ul><li>Add new annotations </li></ul></ul><ul><li>Data Presentation </li></ul><ul><ul><li>Visualization and Export </li></ul></ul>Parameters recorded in Application’s datastore CONTROL Analyse Import Data Present VAMSAS Map Render Filter Data VAMSAS VAMSAS
  6. 7. VAMSAS Client Sessions <ul><li>VAMSAS client library </li></ul><ul><ul><li>Data exchange ( Many applications connect to one document ) </li></ul></ul><ul><ul><ul><li>Locked IO </li></ul></ul></ul><ul><ul><ul><li>Transport objects to/from document </li></ul></ul></ul><ul><ul><ul><li>Object ID queries </li></ul></ul></ul><ul><ul><ul><li>IO streams for application’s own data </li></ul></ul></ul><ul><ul><li>Session Events Handler Chains </li></ul></ul><ul><ul><ul><li>Document updates </li></ul></ul></ul><ul><ul><ul><li>Others join or leave session </li></ul></ul></ul><ul><li>Client Library is ‘lightweight’ </li></ul><ul><ul><li>Easy to adapt existing programs </li></ul></ul><ul><ul><ul><li>‘ Only’ need to write mapping between VAMSAS and legacy data model </li></ul></ul></ul><ul><ul><li>Easy to make new clients/ add application </li></ul></ul>Existing bioinformatics application. VAMSAS Client API adaptor VAMSAS
  7. 8. My work <ul><li>Integrates the AstexViewer@MSD-EBI in VAMSAS workflow. </li></ul><ul><ul><li>Conversion/Proceeding of Data </li></ul></ul><ul><ul><li>Export from AV-MSD </li></ul></ul><ul><ul><li>(annotations for other vamsas application) </li></ul></ul>Separated/specific application (VAMAV) [email_address] [email_address] VAMSAS Client API adaptor
  8. 9. Conversion of data from VAMSAS document <ul><ul><li>Input of the AstexViewer@MSD-EBI: </li></ul></ul><ul><ul><ul><li>Atribute file (Grouping Information) </li></ul></ul></ul><ul><ul><ul><li>ClustalW/FastA alignment </li></ul></ul></ul><ul><ul><ul><li>PDB files </li></ul></ul></ul>
  9. 10. Process of conversion <ul><li>Extract Alignment sequences and annotations </li></ul><ul><li>Mapping with PBD ID </li></ul><ul><li>Sequence Grouping </li></ul><ul><li>Generate required files (atribute, alignment, …) </li></ul><ul><li>Visualise data in AstexViewer@MSD-EBI </li></ul>VAMSAS Document XML – zip Sequence Grouping Generate required files Visualisation in [email_address] Document Processing
  10. 11. Exporting from AV <ul><li>Export of pre-calculated data </li></ul><ul><ul><li>Context dependant </li></ul></ul><ul><ul><ul><li>Ex: Active Site </li></ul></ul></ul><ul><li>Export of functional aspects </li></ul><ul><ul><li>Current Context (as button state) </li></ul></ul>
  11. 12. First Version (18th October 2005) <ul><li>Displays data only from VAMSAS document in the AV@EBI </li></ul><ul><li>Sequence grouping per structure </li></ul><ul><li>Java 1.5 </li></ul><ul><li>Socket communication between the application and AV client </li></ul>
  12. 13. Current version <ul><li>Proper design - Flexibility, configuration </li></ul><ul><li>Session management </li></ul><ul><li>Export of precalculated data: </li></ul><ul><ul><li>Active site export </li></ul></ul><ul><ul><li>BMean </li></ul></ul><ul><li>Sequence grouping per PFAM domain </li></ul><ul><li>Align structures - Rotation Translation Matrix ( SSM – MSD api ) </li></ul><ul><li>Execute ClustalW alignment </li></ul><ul><li>Web interface (JSP, Servlet) , GUI </li></ul>
  13. 14. Future plans <ul><li>Service for grouping/alignment using SSM and ClustalW. </li></ul><ul><li>User management </li></ul><ul><li>Data validation/highlight </li></ul><ul><li>Integrate the new version of the Vamsas client API </li></ul><ul><li>SIFTS initiative – spats web service </li></ul><ul><li>Meeting @ EBI (March 28th-29th) </li></ul><ul><li>E-family </li></ul>
  14. 15. Demonstration <ul><li>VAMSAS @ EBI </li></ul>