XMLBased Grid Data System for Bioinformatics Development

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XML-Based Grid Data System for Bioinformatics
Development

• Noppadon Khiripet, Ph.D
• Wasinee Rungsarityotin, MS
• Chularat Tanprasert, Ph.D
• Royol Chitradon Ph.D

National Electronics and Computer Technology
Center, Thailand
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APBioNet Resources

• BioDatabases
• - BioMirrors, PDB Mirror, SRS
• BioComputing
• Beowulf Linux cluster, BioNavigator, Vector NTI,
• BioTraining
• S Life Science Informatics Alliance, Hypercourse
  in Online Bioinformatics
• Etc.

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APBioNet BioDatabases
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Whats missing ?
I have a bioinformatics question. How do I search
the answer ?
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Sample Question
What proteins in rice have families with a size
greater than twenty members with at least one
known structure, whose corresponding gene
expression is activated under dry conditions, and
that are involved in interactions with at least
two other proteins ?
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Query Mechanism
Whats the communication protocol ?
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eXtensible Markup Language (XML)

• Standard language of data exchange
• Very flexible for defining complex data
  structures
• Many supported tools such as XSL, DOM, Perl, and
  JAVA
• Less overhead when transform data from one to the
  other formats

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XML-Based Grid Data System for Bioinformatics

• lt?xml version"1.0" encoding"UTF-8" ?gt
• lt!DOCTYPE METASERVER_QUERYgt
• ltSEARCHgt
• ltkeygtproteinlt/keygt
• ltcriteria"family size"gt20lt/criteriagt
• ltcriteria"known structure"gt1lt/criteriagt
• ltcriteria"gene expression condition"gtdrylt/cri
  teriagt
• lt!-- This quality will be matched to a
  quantity equivalent to being dry --gt
• ltcriteria"protein interactions"gt2lt/criteriagt
  
• lt/SEARCHgt

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Grid Data System

• Grid technologies such as Globus enables sharing
  of geographically distributed content
• Create a virtual resource of biological data
• Our interest overlaps with the Commodity Grid
  Project
• Exporting Grid technologies to our applications

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Motivating Example Alliance Science Portal, CoG
Kit

• What we have learned about Commodity Grid
• Access and communicate with a variety of
  information sources
• Ability to include remote computational resources
• Performance guarantees
• Portable user interfaces

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Basic Integrated Grid Architecture
Gene finding
Protein Prediction

Applications
Applications Toolkits

Data Grid
Remote Computation
Portals
Grid Services (Middleware)
Protocols, Authentication, Policy, Resource
Management, Discovery, Events, etc.
Grid Fabric (Resources)
Storage Networks, Computer, Display Devices, etc.
and associated local services
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How To Use Grid?
Web Interface
Remote Data analysis service
Applications Toolkits
Genbank, EMBL, BLASTDB, etc..
Commodity Grid Toolkits
Grid Services Fabric
Low-level Grid Technologies
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CoG Mapping to Grid fabric and services
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Our Application Rice

• Building a genomic framework for research in rice
• Providing information and computational resources

In collaboration with DNA Technology
Laboratory, Kasetsart University and
Computational Biology Research Group, University
of Washington
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Our focus on Grid technology

• Low-level utility components
• Build Data cache/replication as an application
  toolkit in the integrated Grid architecture
• Application-specific GUI components
• A query interface for the genomic framework for
  rice research on the top layer (application) of
  Grid architecture

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Questions ?