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

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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 https://vip.creatis.insa-lyon.fr Web portal Infrastructure

  1. 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

  2. https://vip.creatis.insa-lyon.fr Web portal Infrastructure Application as a service File transfer to/from grid Supported by EGI Infrastructure Uses biomed VO (~65 sites in Europe and beyond) Available in N4U (Neugrid) portal VIP consumes ~3 0 CPU years every month France-Grilles Scientific applications DIRAC Cancer therapy simulation Neuro-image analysis 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 Prostate radiotherapy plan simulated Brain tissue segmentation with GATE(L. Grevillot and D. Sarrut) with Freesurfer Image simulation Modeling and optimization of distributed computing systems Echocardiography simulated with Acceleration yielded by non-clairvoyant FIELD-II (O. Bernard et al ) task replication (R. Ferreira da Silva et al )

  3. Infrastructure: EGI's biomed VO ● Important resources ● ~15,000 job slots ● 5 PB storage Distributed in ~65 sites ● http://lsgc.org ● 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 ● 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) 3/10

  4. VIP architecture 0. Login 3. Launch workflow 1. Send input data User Workflow Engine Web Portal (Moteur + GASW) 2. Transfer 4. Generate and input files submit task Storage Element 7. Get files 6. Get task 8. Execute Pilot Manager 9. Upload results (DIRAC) 5. Submit Computing site pilot jobs 4/10

  5. Data sharing ■ Home and team directories ■ Manager and member roles (read, write, delete) Manager Manager Members Members Team 1 Team 2 5/10

  6. Tools available ● Simulation Gate (nuclear medicine, multi-modality) ● Sindbad (CT) ● ● SimuBloch (MRI) FIELD-II, CREANUIS (US) ● ● PET-SORTEO (PET) Treatment planning of ethmoid tumor (in red) using ● Neuroimaging 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 FSL (7 tools) ● Freesurfer (2 tools) ● ● France-Life Imaging tools Brain tissue segmentation with Freesurfer ● Other MRI RF Characterization ● Liver cartography ● Hepatic perfusion index (%) Credits: B. Leporq, O Beuf 6/10

  7. Tool integration through Boutiques Your tool? VIP Virtual Imaging Platform http://vip.creatis.insa-lyon.fr Tool Niak / description PSOM (JSON) http://cbrain.mcgill.ca Tool implementation http://pegasus.isi.edu Workflow Management System for Science Automation http://boutiques.github.io 7/10

  8. A network of platforms (under development) France Life-Imaging ● Common APIs for invoking pipelines, retrieving analyses, querying data ● Common repositories of tools and data

  9. 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

  10. Thank you for your attention! Questions ?

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