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g-INFO portal
Doan Trung Tung
Aurélien BERNARD, Ana Lucia DA-COSTA, Vincent BLOCH, Thanh-Hoa LE, Yannick LEGRE, Lydia MAIGNE, Jean SALZEMANN, Hong-Quang NGUYEN, Vincent BRETON
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g-INFO portal Doan Trung Tung Aurlien BERNARD, Ana Lucia DA-COSTA, - - PowerPoint PPT Presentation
g-INFO portal Doan Trung Tung Aurlien BERNARD, Ana Lucia DA-COSTA, - - PowerPoint PPT Presentation
g-INFO portal Doan Trung Tung Aurlien BERNARD, Ana Lucia DA-COSTA, Vincent BLOCH, Thanh-Hoa LE, Yannick LEGRE, Lydia MAIGNE, Jean SALZEMANN, Hong-Quang NGUYEN, Vincent BRETON 1 Outline Introduction Overview of g-INFO
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Why g-INFO?
H5N1 (avian flu)
262 deaths 436 cases
WHO - July 2009
287 deaths 486 cases
WHO – March 2010
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Influenza surveillance
Data collection
- BioHealthBase
- NCBI
- LosAlamos
Data processing in batch mode
- General phylogenetic
pipelines
- Specific phylogenetic
pipelines Deployment of phylogenetic tools on clusters / grids g-INFO: Grid-based International Network for Flu Oservation
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g-INFO’s overview Global Surveillance Network
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g-INFO’s goals
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Integration of influenza virus data sources into a federation of databases Automatic phylogenetic pipelines Specific molecular epidemiology studies
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Architecture of g-INFO system
- Each data provider has
its own server(s) to store his data
- Data provider export
- nly selected data to a
data grid interface server
- The data exported is
integrated in a common schema on the interface servers
- Providers can keep the
privilege of granting access rights to their data
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Architecture of g-INFO system
- Epidemiologic pipelines
will be deployed on the grid
BLAST Alignment Phylogenetic trees Visualisation ... and more
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g-INFO’s implementation Phylogenetic workflow
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Data collection
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Grid DB
Daily updates
FTP NCBI
Metadata Sequences
Protein, Nucleotide, Coding region
IDs
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WISDOM Production Environment
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Integration of g-INFO into WPE
12 Data collection Data service Amga MUSCLE PhyML Gblocks BLAST Task Manager Job Manager WISDOM Information System Amga Job Submitter g-INFO Data Manager
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Automatic phylogenetic pipeline
13 g-INFO database g-INFO pipeline Task Manager Job Job Manager Job Job Wisdom IS g-INFO portal
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Automatic phylogenetic pipeline
> Run daily a phylogenetic workflow on the grid
AMGA
Metadata Sequences
Protein, Nucleotide, Coding region
IDs
Grid portal
Prepare Data in correct format
Alignment + Curation (Muscle + Gblocks)
NCBI
Phylogenetic Analysis (PhyML) Visualisation tool
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Manual phylogenetic workflow
15 g-INFO database MOTEUR web services Task Manager Job Job Manager Job Job Wisdom IS g-INFO portal MOTEUR desktop tool
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Workflow execution example
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g-INFO portal Phylogenetic workflow
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g-INFO portal
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Collaboration among IFI, IOIT and HPC: IFI: web services to interact between the portal and the system IOIT: design and develop the portal HPC: visualization tool Technologies: JSF 2.0, Ajax, web services, Java aplet, …
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g-INFO portal
19 g-INFO database MOTEUR web services Task Manager Job Job Manager Job Job Wisdom IS g-INFO portal Intermediate web services JSF 2.0 Web services Ajax JDBC
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g-INFO portal – home page
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g-INFO portal - search
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g-INFO portal – search results
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g-INFO portal – search results
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g-INFO portal – working sessions
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g-INFO portal – define working session template
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g-INFO portal – define working session template
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g-INFO portal – define working session template
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g-INFO portal – define working session template
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g-INFO portal – run working session
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g-INFO portal – run working session
Pipeline01 WorkingSession Pipeline02 Pipeline03 Pipeline04 PipelineN Input01 Input02 Input03 inputN result01 result02 result03 result04 resultN
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g-INFO portal – visualization
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Conclusions
A success in terms of international collaboration An example of developping grid application in Vietnam A complementary service for the public health research community
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Perspectives
Provide more tools and pipelines Import other database resources Improve system’s performance We are expecting the research community to contribute with more useful tools Can be applied for other emerging diseases
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Thank you!
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