An Introduction

1. BIO MAJ
WORKFLOW ENGINE DEDICATED TO BIO-DATA
SYNCHRONIZATION AND
PROCESSING.
Sana Anam Roll # 3003
Bs(Hons) Botany 3rd semester Eve
Submitted to Inam ul Haq
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2. CONTENT
 INTRODUCTION
 BACKGROUND OF BIOMAJ
 APPLICATION
 BIOMAJ PROVIDE
 CONCLUSION
 REFRENCES
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3. INTRODUCTION
 In biocomputing,
 analyses are almost systematically reliant on
databanks.
 Any biocomputing site therefore needs to manage
these invaluable databanks that hold a huge
amount of information usually several terabytes,
spread over various international sites and in a
consistent format (there are still several different
standards currently).
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4. BACKGROUND OF BIOMAJ
 The BioMAJ project came out of the work of three teams in 2005: INRIA
Rennes and INRA
 Toulouse and JouyenJosas.
 At the time, no free applications met users’ requirements. The closest
 application was citrina, developed by Josh Goodman (from Washington
University’s gmod project).
 This was a promising prototype – nonetheless quite far from the
application required – and it had
 not been updated since 2004.
 In 2006, these teams (INRIA and INRA) developed a new engine called
BioMAJ1. Based on
 citrina 0.51, nearly all the code was rewritten and the application’s
architecture and functions were
 completely rethought and considerably extended.
 During 2007, the application was tested on the three sites involved in the
project to make it
 more robust and suitable
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5. APPLICATION
 Synchronization :
Multiple remote protocols (ftp, sftp, http, rsync,
local copy)
Data transfers integrity check
Release versioning using a incremental
approach
Multi threading
Data extraction (gzip, tar, bzip)
Data tree directory normalization
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6.  Pre &Post processing :
Advanced workflow description (D.A.G) using
Easy normalized syntax language
Post-process indexation for various
bioinformatics software (blast, srs, fastacmd,
readseq, etc…)
Easy integration of personal scripts for bank
post-processing automation
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7.  Supervision :
Administration web interface
Repository statistics
Mail alerts for the update cycle supervision
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8. BIOMAJ PROVIDE
 A reliable workflow engine that can download
remote data automatically and intelligently
 (error correction, synchronization of local and
remote data), apply formatting to this data and
 put it into production (make the data available for all
users and/or applications).
 A group of predefined workflows for the main
biological banks.
 An indexing scripts library (formatting for
biological data)
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9. CONCLUSION
 BioMAJ provides flexibility in managing banks of
sequences on a site while allowing for rapid
implementation of new workflows by simply creating
a bank description file.
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10. REFERENCES
 Website: http://biomaj.genouest.org/
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Authors: David Allouche, Olivier Filangi , Romaric Sabas,
Olivier Sallou
(olivier.sallou@irisa.fr)