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

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.

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.

Bringing three programs together… 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

Bringing three programs together…

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 BIOLOGICAL SEQUENCE AND ANALYSIS DATA JALVIEW DATA ASTEXVIEWER DATA TOPALI DATA References Provenance

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

VAMSAS Applications VAMSAS 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 Parameters recorded in Application’s datastore CONTROL Analyse Import Data Present VAMSAS Map Render Filter Data VAMSAS VAMSAS

VAMSAS 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

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 VAMSAS

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

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) [email_address] [email_address] VAMSAS Client API adaptor

Integrates the AstexViewer@MSD-EBI in VAMSAS workflow.

Conversion/Proceeding of Data

Export from AV-MSD

(annotations for other vamsas application)

Conversion of data from VAMSAS document Input of the AstexViewer@MSD-EBI: Atribute file (Grouping Information) ClustalW/FastA alignment PDB files

Input of the AstexViewer@MSD-EBI:

Atribute file (Grouping Information)

ClustalW/FastA alignment

PDB files

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 VAMSAS Document XML – zip Sequence Grouping Generate required files Visualisation in [email_address] Document Processing

Extract Alignment sequences and annotations

Mapping with PBD ID

Sequence Grouping

Generate required files (atribute, alignment, …)

Visualise data in AstexViewer@MSD-EBI

Exporting from AV Export of pre-calculated data Context dependant Ex: Active Site Export of functional aspects Current Context (as button state)

Export of pre-calculated data

Context dependant

Ex: Active Site

Export of functional aspects

Current Context (as button state)

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

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

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

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

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

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

Demonstration VAMSAS @ EBI

VAMSAS @ EBI