Transcript Biogrid presentation for APAN26 - NZ

Natjaree Preechaveerakul 1, Unitsa Sungket 3, Kasikrit Damkliang 1,
Pichaya Tandayya 1, 2, Amornrat Phongdara 3 and Pitipol Meemak 3
PSU Grid Centre, Prince of Songkla University 1
Department of Computer Engineering, Prince of Songkla University 2
Center for Genomics and Bioinformatics Research, Prince of Songkla University 3
APAN26 - 6 Aug 2008,
Queenstown, NZ
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BioGrid Team
Prince of Songkla University
• Computer Engineering Department,
Faculty of Engineering
• Center for Genomics and Bioinformatics Research,
Faculty of Science
BioGrid Project
APAN26 - 6 Aug 2008,
Queenstown, NZ
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Funding
This project has been funded by Thai National
Grid Center (TNGC) under Software Industry
Promotion Agency (SIPA).
BioGrid Project
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Objectives
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To build BioGrid infrastructure for Thailand
To build a research network in Bioinformatics
To navigate the Grid usage in Bioinformatics
To build new researchers in Bioinformatics
To promote the myGrid technology
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Queenstown, NZ
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Accomplishments
• Software Installation and Support:
– MPIBlast
– Bio Roll
– Bio Portal
– Taverna
• Training: related workshops
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Background: Bioinformatics
• Apply computer technology to biological information
• gather, store, analyze and integrate biological and
genetic information such as nucleotide and amino acid
sequences
• Example applications:
• gene-based drug discovery and development
• Multidiscipline:
• Biology, Computer Science, Mathematics and
Information Technology
BioGrid Project
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Queenstown, NZ
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MPIBlast
http://www.mpiblast.org/
• A Message Passing Interface - Basic Local Alignment Search
Tool,
• Uses the parallel implementation of NCBI BLAST,
• Efficiently utilizes distributed computational resources through
database fragmentation, query segmentation, intelligent
scheduling, and parallel I/O,
• Improves NCBI BLAST performance by several orders of
magnitude while scaling to hundreds of processors.
BioGrid Project
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Queenstown, NZ
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MPIBlast Databases on TNGC
The below databases are on service on the Tera Cluster
of the Thai National Grid Center.
nr: Non-redundant protein sequence database
nt: Not non-redundant nucleotide database
Etc.
BioGrid Project
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Queenstown, NZ
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Bio Portal on TNGC
The pioneer portal on the the Tera Cluster of the Thai
National Grid Center uses
• Gridsphere portal framework
• MPI-Blast service
http://tera.thaigrid.or.th:8081/gridsphere
Contact: [email protected]
BioGrid Project
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Queenstown, NZ
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Bio Grid Infrastructure
Bio Grid services include web services,
portals, command line tools.
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Queenstown, NZ
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BioGrid Project
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Queenstown, NZ
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Taverna
– Free software tool
– Support various platform
– For designing and executing workflows
http://taverna.sourceforge.net/
BioGrid Project
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Queenstown, NZ
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What is a Workflow?
A set of components
and relations between
them used to define a
complex process from
simple building blocks
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Queenstown, NZ
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Fussy Old Cut-and-paste Method
• Various
services and
databases are
distributed and
so different in
standards
• Cutting and Pasting between web pages in each window of browser needs
labor, iteration and is difficult to verify
• Can not apply to a large scale of research
nor fulfill the scientific expectation
BioGrid Project
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Queenstown, NZ
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Advantages of Using Workflows
• High-level abstraction
• Easier to understand and modify.
• Easier to describe and discuss
with others.
• Describes what you want to do,
not how to do it.
• Automation
• Sharing and re-use
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Queenstown, NZ
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Components in Taverna
• Reusable building block which performs
some well defined function within a process,
• Computational resource accessible
via the internet or on user's local
work station, web services, command line tool,
and perl scripts
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Queenstown, NZ
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Our Work: Thai Taverna documents
• Installation
• Composition
• Plugins
• Example
• Etc.
BioGrid Project
http://biogrid.coe.psu.ac.th
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Queenstown, NZ
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Taverna and BioGrid Workshops
Speakers:
• Prof. Dr. Andy Brass, and Dr. Katy Wolstenkroft
from University of Manchester
• Assoc. Prof. Dr. Wasan Jantratit and Akawat Pasomsap from
Mahidol University (MU)
• Asst.Prof.Dr. Pichaya Tandayya and Unitsa Sungket from
Prince of Songkla University (PSU)
• Assoc. Prof. Dr. Chokchai Leangsuksun, from
Louisiana Tech University (LSU)
Venues:
PSU, MU, CMU, KU
BioGrid Project
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Queenstown, NZ
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Demo
•Bio Portal
•Taverna
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Queenstown, NZ
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Software and Services Provided
• MPIBlast and Bio Roll on the Tera Cluster and at the
clusters of Thai National Grid Members
– Command line service
• Bio Portal on the Tera Cluster of TNGC
– MPIBlast service
• Taverna on the Tera Cluster and at the clusters of
Thai National Grid Members
– Local Web services at any cluster for faster processing in
Taverna workflow
– Taverna manual document in Thai
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Queenstown, NZ
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List of Software
– Command line service
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MPIBlast
FASTA
ClustalW
Emboss
Glimmer
biopython
MrBayes
Phylip
BioGrid Project
– Bio Portal
• MPIBlast service
– Taverna
– Local web services for
Taverna
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Examples of BioGrid’s Usage
• Pharmacogenomics
• shrimp SNPs analysis
• Statistic Computation on Genome Wide
Association Study
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Acknowledgements
• Prof. Dr. Carole Goble and myGrid team members, School of
Computer Science at the University of Manchester for Taverna
Training
• Yossatorn Phumisut from Manakorn University for Grid Sphere
Knowledge
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Information
Office:
2nd floor, Robot Building, Department of Computer
Engineering, Prince of Songkla University,
P.O. Box 2, Kohong, Hatyai, Songkhla 90112
Contact: [email protected]
Website: http://biogrid.coe.psu.ac.th
Tel:
+66 74-287374
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Queenstown, NZ
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