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

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.

APBioNet BioDatabases

What’s missing ? I have a bioinformatics question. How do I search the answer ?

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 ?

Query Mechanism Meta Server 1.Find genes in rice 2.Apply genes to protein DB 3.Check with known structures 4.Link to Gene expression DB 5.Link to 2-hybrid data 6.Link to functional annotation data QueriesResults What’s the communication protocol ?

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

XML-Based Grid Data System for Bioinformatics protein dry 2+

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

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

Basic Integrated Grid Architecture Protocols, Authentication, Policy, Resource Management, Discovery, Events, etc. Protocols, Authentication, Policy, Resource Management, Discovery, Events, etc. Gene finding Gene finding Protein Prediction Protein Prediction Grid Services (Middleware) Grid Fabric (Resources) Applications Toolkits Data Grid Remote Computation Portals … … Storage Networks, Computer, Display Devices, etc. and associated local services

How To Use Grid? Commodity Grid Toolkits Low-level Grid Technologies Web Interface Genbank, EMBL, BLASTDB, etc.. Remote Data analysis service Local Data analysis service Applications & Toolkits Grid Services & Fabric

CoG Mapping to Grid fabric and services

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

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

Questions ?