1st EELA Grid School 1st EELA Grid School December 15th of 2006December 15th of 2006

Eduardo MURRIETA LEON

Romualdo ZAYAS-LAGUNAS

Pierre-Alain BRANGER

Jérôme VERLEYEN

Roberto RODRIGUEZ

César BONAVIDES

Alfredo HERNANDEZ

EMBOSS over a GridEMBOSS over a Grid

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EMBOSS over a GridEMBOSS over a Grid

• 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

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EMBOSS over a GridEMBOSS over a Grid

Plan APlan A

UI

BDII

CE WNs

RB

InputSandbox InputSandbox includes:includes: Binary programBinary program DB ( big files!)DB ( big files!)

Bad performanceBad performance

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EMBOSS over a GridEMBOSS over a Grid

Plan BPlan B

UI

BDII

CE WNs

RB

DB & application on DB & application on each WNeach WN

Use of TAGsUse of TAGs DB redundancy!DB redundancy! Complex to update!Complex to update!

?

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EMBOSS over a GridEMBOSS over a Grid

Plan B.1Plan B.1

UI

BDII

CE WNs

RB

NFS

DB & application DB & application shared by WNsshared by WNs

Easy to Update DBEasy to Update DB Each CE needs DB!Each CE needs DB! NFS installed on NFS installed on

WNsWNs

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EMBOSS over a GridEMBOSS over a Grid

Plan CPlan C

UI

BDII

CE WNs

RBSE

GFAL

NFS Use of GFAL API:Use of GFAL API: Wrapping streams functions Wrapping streams functions

(works)(works) Now supports files bigger than Now supports files bigger than

2GB when necessary2GB when necessary

Direct replacement of system Direct replacement of system calls in the memory map of calls in the memory map of the program (working on)the program (working on)

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EMBOSS over a GridEMBOSS over a Grid

EMBOSS workflow on EMBOSS workflow on “Lost Island GRID”“Lost Island GRID”

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DISTANCE

PARSIMONY

M. LIKELIHOOD

CONSENSUS

EXTRACT SEQ

ALIGMENT

Use of Scripting Use of Scripting techniques (DAG – techniques (DAG – like jobs)like jobs)

Complex for final userComplex for final user

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EMBOSS over a GridEMBOSS over a Grid

Original ObjectivesOriginal 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

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EMBOSS over a GridEMBOSS over a Grid

New objectivesNew objectives

Implementation on the “Lost land of Mexico”Implementation on the “Lost land of Mexico”

Creation of “EMBOSS over a Grid” rpmsCreation of “EMBOSS over a Grid” rpms

EMBOSS portal using Genius + wEMBOSSEMBOSS portal using Genius + wEMBOSS

Workflow controlled through R-GMAWorkflow controlled through R-GMA

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EMBOSS over a GridEMBOSS over a Grid

Muito obrigado!Muito obrigado!

EELA committee organizerEELA committee organizer

TutorsTutors

Support staffSupport staff

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EMBOSS over a GridEMBOSS over a Grid

Bye ItacuruBye Itacuruçaça

Click here

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EMBOSS over a GridEMBOSS over a Grid