1 / 12

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

charles-carney
Download Presentation

1st EELA Grid School

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related