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Funded by: VAMSAS Project September 1rt, 2005 – February 2006 Pierre Marguerite

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Page 1: Group Meeting Vamsas Project Final

Funded by:

VAMSAS Project

September 1rt, 2005 –February 2006

Pierre Marguerite

Page 2: Group Meeting Vamsas Project Final

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.

Page 3: Group Meeting Vamsas Project Final

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

Page 4: Group Meeting Vamsas Project Final

Funded by:

9th February 2006

Pierre Marguerite - VAMSAS Project4

Page 5: Group Meeting Vamsas Project Final

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

Page 6: Group Meeting Vamsas Project Final

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

Page 7: Group Meeting Vamsas Project Final

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

Page 8: Group Meeting Vamsas Project Final

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

Page 9: Group Meeting Vamsas Project Final

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

Page 10: Group Meeting Vamsas Project Final

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

Page 11: Group Meeting Vamsas Project Final

Funded by:

9th February 2006

Pierre Marguerite - VAMSAS Project1

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Exporting from AV

• Export of pre-calculated data– Context dependant

• Ex: Active Site

• Export of functional aspects– Current Context (as button state)

Page 12: Group Meeting Vamsas Project Final

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

Page 13: Group Meeting Vamsas Project Final

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

Page 14: Group Meeting Vamsas Project Final

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

Page 15: Group Meeting Vamsas Project Final

Funded by:

9th February 2006

Pierre Marguerite - VAMSAS Project1

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Demonstration

VAMSAS @ EBI