Upload
charles-carney
View
44
Download
0
Tags:
Embed Size (px)
DESCRIPTION
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 - PowerPoint PPT Presentation
Citation preview
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
2
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
3
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
4
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!
?
5
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
6
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)
7
EMBOSS over a GridEMBOSS over a Grid
EMBOSS workflow on EMBOSS workflow on “Lost Island GRID”“Lost Island GRID”
1 2
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
8
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
9
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
10
EMBOSS over a GridEMBOSS over a Grid
Muito obrigado!Muito obrigado!
EELA committee organizerEELA committee organizer
TutorsTutors
Support staffSupport staff
11
EMBOSS over a GridEMBOSS over a Grid
Bye ItacuruBye Itacuruçaça
Click here
12
EMBOSS over a GridEMBOSS over a Grid