1. The BioBox Initiative: Bio-ClusterGrid Maddie Wong Technical Marketing Engineer Sun APSTC – Asia Pacific Science & Technology Center

2. 02 April 2004 ©Maddie Wong, Technical Marketing Engineer, Sun APSTC 1 Agenda Bio-ClusterGrid: Introduction Bio-ClusterGrid: Benefits Solaris 9 Operating Environment Sun Grid Engine (SGE) Grid Engine Portal (GEP) Applications on Bio-ClusterGrid Current and Future Developments Demonstration

3. 02 April 2004 ©Maddie Wong, Technical Marketing Engineer, Sun APSTC 1

4. 02 April 2004 ©Maddie Wong, Technical Marketing Engineer, Sun APSTC 1 Bio-ClusterGrid: Introduction 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. 02 April 2004 ©Maddie Wong, Technical Marketing Engineer, Sun APSTC 1 Bio-ClusterGrid: Benefits Fast setup (2 ½ – 3 hours) –Installation of Solaris 9 Operating System –Installation of the 28 Bioinformatics applications –Activation of Sun Grid Engine –Installation and Activation of Grid Engine Portal

6. 02 April 2004 ©Maddie Wong, Technical Marketing Engineer, Sun APSTC 1 Bio-ClusterGrid: Benefits Compared to Manual Installation –Installation Of Solaris 9 ( 30 – 40 minutes) –Downloading, compiling and installation of 28 bioinformatics applications (1 week) –Installation and Configuration of Sun Grid Engine (1 day) –Installation and Configuration of Grid Engine Portal ( 1 day)

7. 02 April 2004 ©Maddie Wong, Technical Marketing Engineer, Sun APSTC 1 Bio-ClusterGrid: Benefits Huge savings in time for administrators No need to deal with the complexity of compilation : compilation errors, checking for installing dependencies SGE and GEP installations can be confusing for unfamiliar user

8. 02 April 2004 ©Maddie Wong, Technical Marketing Engineer, Sun APSTC 1 Solaris 9 Operating Environment Latest version of Sun Solaris Supports GNOME 2.0 Desktop Environment Improvements in Performance, Security

9. 02 April 2004 ©Maddie Wong, Technical Marketing Engineer, Sun APSTC 1 GNOME 2.0 Desktop Environment

10. 02 April 2004 ©Maddie Wong, Technical Marketing Engineer, Sun APSTC 1 Sun Grid Engine Distributed Resource Management Software Provides load balancing and resource management Supports running of parallel applications over a cluster

11. 02 April 2004 ©Maddie Wong, Technical Marketing Engineer, Sun APSTC 1 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)

12. 02 April 2004 ©Maddie Wong, Technical Marketing Engineer, Sun APSTC 1 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.

13. 02 April 2004 ©Maddie Wong, Technical Marketing Engineer, Sun APSTC 1 Grid Engine Portal

14. 02 April 2004 ©Maddie Wong, Technical Marketing Engineer, Sun APSTC 1 Submitting BLAST job using GEP

15. 02 April 2004 ©Maddie Wong, Technical Marketing Engineer, Sun APSTC 1 Blast Job Output on GEP

16. 02 April 2004 ©Maddie Wong, Technical Marketing Engineer, Sun APSTC 1

17. 02 April 2004 ©Maddie Wong, Technical Marketing Engineer, Sun APSTC 1 Current Development ● Linux and Solaris x86 Versions of Bio- ClusterGrid Future Developments ● Bio-Server (Bioinformatics databases server) ● Improvements to GEP interface in terms of functionality and user-friendliness

18. 02 April 2004 ©Maddie Wong, Technical Marketing Engineer, Sun APSTC 1 BioBox Engineering Team ● Headed by Simon See ● Gilbert Thomas ● Maddie Wong ● Deepak Jeevan Kumar ● APSTF Interns (IIT Delhi, India) For more info, visit http://apstc.sun.com.sg/biobox.php

19. Demonstration For more queries ask-apstc@sun.com