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1st EELA Grid School

EMBOSS over a Grid. Eduardo MURRIETA LEON Romualdo ZAYAS-LAGUNAS Pierre-Alain BRANGER Jérôme VERLEYEN Roberto RODRIGUEZ César BONAVIDES Alfredo HERNANDEZ. 1st EELA Grid School. December 15th of 2006. The E uropean M olecular B iology O pen S oftware S uite - From EMBNet

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1st EELA Grid School

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  1. EMBOSS over a Grid Eduardo MURRIETA LEON Romualdo ZAYAS-LAGUNAS Pierre-Alain BRANGER Jérôme VERLEYEN Roberto RODRIGUEZ César BONAVIDES Alfredo HERNANDEZ 1st EELA Grid School December 15th of 2006

  2. The European Molecular Biology Open Software Suite • - From EMBNet • - We are EMBNet Mexico • Is a set of programs to analyze genetic sequence • a toolkit for creating robust bioinformatics applications or workflows • Database searching

  3. Plan A • InputSandbox includes: • Binary program • DB ( big files!) • Bad performance UI CE WNs BDII RB

  4. ? Plan B • DB & application on each WN • Use of TAGs • DB redundancy! • Complex to update! UI CE WNs BDII RB

  5. NFS Plan B.1 • DB & application shared by WNs • Easy to Update DB • Each CE needs DB! • NFS installed on WNs UI CE WNs BDII RB

  6. NFS Plan C • Use of GFAL API: • Wrapping streams functions (works) • Now supports files bigger than 2GB when necessary • Direct replacement of system calls in the memory map of the program (working on) UI CE WNs GFAL BDII RB SE

  7. 1 2 EMBOSS workflow on “Lost Island GRID” DISTANCE • Use of Scripting techniques (DAG – like jobs) • Complex for final user CONSENSUS EXTRACT SEQ ALIGMENT PARSIMONY M. LIKELIHOOD

  8. Original Objectives • « Get EMBOSS running over a Grid » • - EMBOSS jobs execution on a grid through command line • - Retrieving jobs results • - Be able to execute a complete workflow / pipeline sequence analysis • Complementary functions • EMBOSSed Databases research • Wrapping applications for EMBOSS over a Grid • Web interface and Project manager for EMBOSS • Have a BioGrid portal

  9. New objectives • Implementation on the “Lost land of Mexico” • Creation of “EMBOSS over a Grid” rpms • EMBOSS portal using Genius + wEMBOSS • Workflow controlled through R-GMA

  10. Muito obrigado! • EELA committee organizer • Tutors • Support staff

  11. Bye Itacuruça Click here

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