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Funded by:
VAMSAS Project
September 1rt, 2005 –February 2006
Pierre Marguerite
Funded by:
9th February 2006
Pierre Marguerite - VAMSAS Project2
What is VAMSAS?• 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.
Funded by:
9th February 2006
Pierre Marguerite - VAMSAS Project3
JalviewAlignment Visualization
Sequence Analysis(University of Dundee
Geoff Barton & David MartinJim Procter, Andrew Waterhouse)
Bringing three programs together…
TOPAliDNA Recombination
Phylogenetic Analysis(Biomathematics and Statistics Scotland (BioSS)
At Scottish Crop Research Institute (SCRI)Frank Wright & David Marshall
Iain Milne)
AstexViewer@EBIMolecular Graphics
Conformation AnalysisReaction Diagrams (Tom Oldfield & Kim Henrick
Pierre Marguerite)
The VAMSAS FrameworkVisual Analysis of Molecular Sequences, Alignments and Structures
http://www.vamsas.ac.uk
Funded by:
9th February 2006
Pierre Marguerite - VAMSAS Project4
Funded by:
9th February 2006
Pierre Marguerite - VAMSAS Project5
The VAMSAS Document
• XML model for core biological data types and annotation
– Database-like primary keys
• Provenance for primary and derived data
– What was done and when
• References for primary data
– Sequence IDs– Database cross references
• Data storage for each VAMSAS application
JALVIEW DATAASTEXVIEWER
DATATOPALI DATA
BIOLOGICAL SEQUENCE AND ANALYSIS DATA
References
Provenance
Funded by:
9th February 2006
Pierre Marguerite - VAMSAS Project6
VAMSAS ApplicationsVAMSAS Apps have three main functions:• Data Import
– Translate data into VAMSAS XML
• Data Analysis– Extend core data set– Add new annotations
• Data Presentation– Visualization and Export
Map
Render
Filter
Parameters recorded in Application’s datastore
CONTROL
Data
Analyse
ImportData
Present
Funded by:
9th February 2006
Pierre Marguerite - VAMSAS Project7
VAMSAS Client Sessions
• VAMSAS client library– Data exchange (Many applications
connect to one document)• Locked IO• Transport objects to/from document• Object ID queries• IO streams for application’s own data
– Session Events Handler Chains• Document updates• Others join or leave session
• Client Library is ‘lightweight’– Easy to adapt existing programs
• ‘Only’ need to write mapping between VAMSAS and legacy data model
– Easy to make new clients/ add application
Existing bioinformatics application.
VAMSAS Client API
adaptor
Funded by:
9th February 2006
Pierre Marguerite - VAMSAS Project8
My work
• Integrates the AstexViewer@MSD-EBI in VAMSAS workflow.– Conversion/Proceeding of Data – Export from AV-MSD
(annotations for other vamsas application)
Separated/specific application (VAMAV)
AstexViewer@MSD-EBI
AstexViewer@MSD-EBI.
VAMSAS Client API
adaptor
Funded by:
9th February 2006
Pierre Marguerite - VAMSAS Project9
Conversion of data from VAMSAS document
– Input of the AstexViewer@MSD-EBI: • Atribute file (Grouping Information)
• ClustalW/FastA alignment
• PDB files
Funded by:
9th February 2006
Pierre Marguerite - VAMSAS Project1
0
Process of conversion• Extract Alignment
sequences and annotations
• Mapping with PBD ID• Sequence Grouping• Generate required files
(atribute, alignment, …) • Visualise data in
AstexViewer@MSD-EBI
Document Processing
VAMSAS DocumentXML – zip
Sequence Grouping
Generate required files
Visualisation in AstexViewer@MSD-EBI
Funded by:
9th February 2006
Pierre Marguerite - VAMSAS Project1
1
Exporting from AV
• Export of pre-calculated data– Context dependant
• Ex: Active Site
• Export of functional aspects– Current Context (as button state)
Funded by:
9th February 2006
Pierre Marguerite - VAMSAS Project1
2
First Version (18th October 2005)
• Displays data only from VAMSAS document in the AV@EBI
• Sequence grouping per structure
• Java 1.5
• Socket communication between the application and AV client
Funded by:
9th February 2006
Pierre Marguerite - VAMSAS Project1
3
Current version• Proper design - Flexibility, configuration• Session management• Export of precalculated data:
– Active site export– BMean
• Sequence grouping per PFAM domain• Align structures - Rotation Translation Matrix
(SSM – MSD api)• Execute ClustalW alignment • Web interface (JSP, Servlet) , GUI
Funded by:
9th February 2006
Pierre Marguerite - VAMSAS Project1
4
Future plans• Service for grouping/alignment using SSM and
ClustalW.• User management• Data validation/highlight• Integrate the new version of the Vamsas client API• SIFTS initiative – spats web service
• Meeting @ EBI (March 28th-29th)• E-family
Funded by:
9th February 2006
Pierre Marguerite - VAMSAS Project1
5
Demonstration
VAMSAS @ EBI
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