Successfully reported this slideshow.
We use your LinkedIn profile and activity data to personalize ads and to show you more relevant ads. You can change your ad preferences anytime.

Group Meeting Vamsas Project Final

430 views

Published on

  • Be the first to comment

  • Be the first to like this

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 ) http://www.vamsas.ac.uk 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>

×