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

2. 04 December 2003 ©Gilbert Thomas, Associate Engineer, Sun APSTC 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. 04 December 2003 ©Gilbert Thomas, Associate Engineer, Sun APSTC 3

4. 04 December 2003 ©Gilbert Thomas, Associate Engineer, Sun APSTC 4 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

5. 04 December 2003 ©Gilbert Thomas, Associate Engineer, Sun APSTC 5 Introduction: Bio-ClusterGrid Fast setup (2 ½ hours) Avoid hassle of downloading, compiling and installing biox applications. Applications optimized for SPARC.

6. 04 December 2003 ©Gilbert Thomas, Associate Engineer, Sun APSTC 6 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

7. 04 December 2003 ©Gilbert Thomas, Associate Engineer, Sun APSTC 7 GNOME 2.0 Desktop Environment

8. 04 December 2003 ©Gilbert Thomas, Associate Engineer, Sun APSTC 8 Sun Grid Engine Distribute Resource Management Software Provides load balancing and resource management Supports running of parallel applications over a cluster

9. 04 December 2003 ©Gilbert Thomas, Associate Engineer, Sun APSTC 9 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)

10. 04 December 2003 ©Gilbert Thomas, Associate Engineer, Sun APSTC 10 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.

11. 04 December 2003 ©Gilbert Thomas, Associate Engineer, Sun APSTC 11 Grid Engine Portal

12. 04 December 2003 ©Gilbert Thomas, Associate Engineer, Sun APSTC 12 Submitting BLAST job using GEP

13. 04 December 2003 ©Gilbert Thomas, Associate Engineer, Sun APSTC 13 Blast Job Output on GEP

14. 04 December 2003 ©Gilbert Thomas, Associate Engineer, Sun APSTC 14 Applications on Bio-ClusterGrid

15. 04 December 2003 ©Gilbert Thomas, Associate Engineer, Sun APSTC 15 1.Homology & Similarity Search 1.Homology & Similarity Search Definition –Sequence similarity is observable, homology is an hypothesis based on observation Applications –BLAST –FASTA –GlimmerM –Wise

16. 04 December 2003 ©Gilbert Thomas, Associate Engineer, Sun APSTC 16 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

17. 04 December 2003 ©Gilbert Thomas, Associate Engineer, Sun APSTC 17 3. Structural Prediction Definition –Determines the 2D/3D structure of proteins Applications –Dowser –FastDNAml –LOOPP –Mapmaker/QTL –PAML –PHYLIP

18. 04 December 2003 ©Gilbert Thomas, Associate Engineer, Sun APSTC 18 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

19. 04 December 2003 ©Gilbert Thomas, Associate Engineer, Sun APSTC 19 5. Development Tools Biojava Bioperl Biopython

20. 04 December 2003 ©Gilbert Thomas, Associate Engineer, Sun APSTC 20 6. Other Software Apache SQL GNU Compilers Sun One Compilers (trial licence) HPC ClusterTools (Sun’s implementation of MPI)

21. 04 December 2003 ©Gilbert Thomas, Associate Engineer, Sun APSTC 21 Bio-ClusterGrid Installation

22. 04 December 2003 ©Gilbert Thomas, Associate Engineer, Sun APSTC 22 Bio-ClusterGrid Installation 1.Flash Archive Installation 2.Sun Grid Engine Installation 3.Grid Engine Portal Installation 4.Grid Installation for Cluster

23. 04 December 2003 ©Gilbert Thomas, Associate Engineer, Sun APSTC 23 1. Solaris 9 Flash Archive Installation

24. 04 December 2003 ©Gilbert Thomas, Associate Engineer, Sun APSTC 24 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.

25. 04 December 2003 ©Gilbert Thomas, Associate Engineer, Sun APSTC 25 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.

26. 04 December 2003 ©Gilbert Thomas, Associate Engineer, Sun APSTC 26 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.

27. 04 December 2003 ©Gilbert Thomas, Associate Engineer, Sun APSTC 27 3. Cluster Grid Installation: ● For every execution node, “run./inst_sge -x - auto” in SGE directory. ● Installation time : Less than 5 minutes

28. 04 December 2003 ©Gilbert Thomas, Associate Engineer, Sun APSTC 28 4.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.

29. 04 December 2003 ©Gilbert Thomas, Associate Engineer, Sun APSTC 29 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

30. 04 December 2003 ©Gilbert Thomas, Associate Engineer, Sun APSTC 30 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

31. 04 December 2003 ©Gilbert Thomas, Associate Engineer, Sun APSTC 31 Future Developments ● Improvement to GEP Installation Procedure ● Bio-Server ● Bio-Workstation

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