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The BioBox Initiative: Bio-ClusterGrid

Gilbert Thomas Associate Engineer Sun APSTC – Asia Pacific Science & Technology Center. The BioBox Initiative: Bio-ClusterGrid. Agenda. Introduction : Bio-ClusterGrid Solaris 9 Operating Environment Sun Grid Engine (SGE) Grid Engine Portal (GEP) Applications on Bio-ClusterGrid

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The BioBox Initiative: Bio-ClusterGrid

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  1. Gilbert Thomas Associate Engineer Sun APSTC – Asia Pacific Science & Technology Center The BioBox Initiative:Bio-ClusterGrid

  2. Agenda Introduction : Bio-ClusterGrid Solaris 9 Operating Environment Sun Grid Engine (SGE) Grid Engine Portal (GEP) Applications on Bio-ClusterGrid Installation of Bio-ClusterGrid Current and Future Developments Questions and Answers

  3. Introduction: Bio-ClusterGrid Grid-enabled Bioinformatics Package Consists of 4 major components Solaris 9 Operating Environment (April 2003 version) Collection of 28 Bioinformatics applications pre-installed and pre-configured Sun Grid Engine Grid Engine Portal

  4. Introduction: Bio-ClusterGrid • Fast setup (2 ½ hours) • Avoid hassle of downloading, compiling and installing biox applications. • Applications optimized for SPARC.

  5. Solaris 9 Operating Environment Latest version of Sun Solaris Supports GNOME 2.0 Desktop Environment Improvements in Performance, Security Easy patch administration using Patch Manager

  6. GNOME 2.0 Desktop Environment

  7. Sun Grid Engine • Distribute Resource Management Software • Provides load balancing and resource management • Supports running of parallel applications over a cluster

  8. Grid Engine Portal • Integrated into Sun One Portal Server • Provides a web interface to some applications running on Sun Grid Engine • Remote access from anywhere, anytime and any computer with a Java-enabled browser. • For users who dislike Command-Line Interface (CLI)

  9. Grid Engine Portal • Job Submission done through customised forms for each application • View results of jobs online and/or download to local machine. • Email user when job is completed.

  10. Grid Engine Portal

  11. Submitting BLAST job using GEP

  12. Blast Job Output on GEP

  13. Applications on Bio-ClusterGrid

  14. 1.Homology & Similarity Search • Definition • Sequence similarity is observable, homology is an hypothesis based on observation • Applications • BLAST • FASTA • GlimmerM • Wise

  15. 2. Sequence Analysis • Definition • Use of bioinformatics methods to determine the biological function and structure of genes and the proteins they code for • Applications • ACT • ClustalW • EMBOSS • HMMER • IMAGE • T-Coffee

  16. 3. Structural Prediction • Definition • Determines the 2D/3D structure of proteins • Applications • Dowser • FastDNAml • LOOPP • Mapmaker/QTL • PAML • PHYLIP

  17. 4. Molecular Imaging/Modeling • Definition • Tools that allow user to make predictions of the secondary structure of proteins arising from a given amino acid sequence. • Applications • Artemis • Cn3D • GROMACS • RasMol • ReadSeq • TribeMCL • VMD

  18. 5. Development Tools • Biojava • Bioperl • Biopython

  19. 6. Other Software • Apache • SQL • GNU Compilers • Sun One Compilers (trial licence) • HPC ClusterTools (Sun’s implementation of MPI)

  20. Bio-ClusterGrid Installation

  21. Bio-ClusterGrid Installation Flash Archive Installation Sun Grid Engine Installation Grid Engine Portal Installation Grid Installation for Cluster

  22. 1. Solaris 9 Flash Archive Installation

  23. 1. Solaris 9 Flash Archive Installation • Flash archive contains the entire OS Image of the machine. • All applications, files on original machine will be replicated on the clone machines upon installation. • Installation of flash archive is much faster than a normal Solaris OE installation.

  24. 1. Solaris 9 Flash Archive Installation • Installed using Solaris 9 Installation CD 04/03 or later • Can be installed from ftp server, DVD, http server.

  25. 2. Sun Grid Engine Installation Very fast; less than 5 minutes per host ./inst_sge -m –fast in SGE directory Must be run by root user.

  26. 3. Cluster Grid Installation: For every execution node, “run ./inst_sge -x -auto” in SGE directory. Installation time : Less than 5 minutes

  27. Grid Installation: Requirements Users using SGE must have unix account on every execution node (e.g. By using NIS) Applications must be installed in all the nodes in the same path (e.g. By using NFS Share) Sun Grid Engine and Grid Engine Portal root directory must be nfs shared.

  28. 3. Grid Engine Portal Installation 3 Step Procedure Installation of Sun One Portal Server Installation of Gateway for Secure Access Installation of Grid Engine Portal Installation takes around 30-40 minutes

  29. Current Developments • Improvement to the GEP Interface • Make it easier and comfortable for biologists to run their applications using GEP • Biologists choose their application and immediately run their job

  30. Future Developments • Improvement to GEP Installation Procedure • Bio-Server • Bio-Workstation

  31. Questions? For more queries ask-apstc@sun.com

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