VIP A Virtual Imaging Platform for the Long Tail of Science Sorina - - PowerPoint PPT Presentation

VIP

A Virtual Imaging Platform for the Long Tail of Science

Sorina POP, Tristan GLATARD

University of Lyon, CNRS, INSERM, CREATIS, France. EGI Community Forum, 11/11/2015

Web portal Users

825 registered users in Sep 2015 Most used robot certificate in EGI in 2012(http://go.egi.eu/wiki.robot.users) 33 publications since 2011 Neuro-image analysis Cancer therapy simulation

Prostate radiotherapy plan simulated with GATE(L. Grevillot and D. Sarrut)

Image simulation

Echocardiography simulated with FIELD-II (O. Bernard et al)

Modeling and optimization of distributed computing systems

Acceleration yielded by non-clairvoyant task replication (R. Ferreira da Silva et al) Brain tissue segmentation with Freesurfer

Scientific applications Infrastructure

Supported by EGI Infrastructure Uses biomed VO (~65 sites in Europe and beyond) Available in N4U (Neugrid) portal VIP consumes ~30 CPU years every month

DIRAC France-Grilles

Application as a service File transfer to/from grid

https://vip.creatis.insa-lyon.fr

Infrastructure: EGI's biomed VO

• Important resources
• ~15,000 job slots
• 5 PB storage
• Distributed in ~65 sites
• Sustained activity
• Operating since 2004
• Technical teams on shift for monitoring and support
• ~3700 CPU years

consumed every year

• Open access
• For non-commercial users
• For life-science applications

http://lsgc.org

3/10

Per-VO distribution of the normalized CPU time consumed by Life-Science VOs in EGI from December 2012 to November 2013 (total: 230,367,332 normalized CPU hours)

VIP architecture

User Web Portal

• 0. Login
• 1. Send input data

Storage Element Workflow Engine (Moteur + GASW)

• 3. Launch workflow

Pilot Manager (DIRAC)

• 4. Generate and

submit task

• 5. Submit

pilot jobs

• 2. Transfer

input files

Computing site

• 6. Get task
• 7. Get files
• 8. Execute
• 9. Upload results

4/10

Team 1 Team 2

Manager Members Manager Members

■ Home and team directories ■ Manager and member roles (read, write, delete)

Data sharing

5/10

Tools available

• Simulation
• Gate (nuclear medicine, multi-modality)
• Sindbad (CT)
• SimuBloch (MRI)
• FIELD-II, CREANUIS (US)
• PET-SORTEO (PET)
• Neuroimaging
• FSL (7 tools)
• Freesurfer (2 tools)
• France-Life Imaging tools
• Other
• MRI RF Characterization
• Liver cartography

Brain tissue segmentation with Freesurfer Hepatic perfusion index (%) Credits: B. Leporq, O Beuf Treatment planning of ethmoid tumor (in red) using

• GATE. The execution corresponds to a total CPU time of

approximately 4.5 months completed with VIP in less than one day. Credits: Yann Perrot

6/10

Tool integration through Boutiques

Tool description (JSON) Tool implementation Workflow Management System for Science Automation http://pegasus.isi.edu Virtual Imaging Platform

VIP

http://vip.creatis.insa-lyon.fr Your tool? Niak / PSOM http://boutiques.github.io http://cbrain.mcgill.ca

7/10

A network of platforms (under development)

• Common APIs for invoking pipelines, retrieving analyses, querying data
• Common repositories of tools and data

France Life-Imaging

Conclusion and Perspectives

■ Biomed

■ Important resources and sustained activity for life-science

applications

■ VIP is used daily to produce scientific results

■ Distributed computing and application sharing ■ Data management and analysis ■ New applications integrated regularly

■ Potential collaborations

■ You are welcome to use VIP and Biomed ■ Interoperability efforts are encouraged

9/10

Thank you for your attention!

Questions ?