APBioNet Workshop on BioBox:
Sun BioClusterGrid, APBioBox and KOOPLite

PreWorkshop Instructions

Aims:
1. To introduce participants to biocomputing on Cluster Grid using BioClusterGrid (for Solaris)
2. To introduce participants to biocomputing on Globus Grid using APBioBox one-stop installation (for Redhat Linux)
3. To introduce participants to BioWorkflow Integration using KOOPLite
4. To offer the opportunity to participate in sharing computational resources on the APBioGrid

• Programme
  • 1300 Registration
  • 1330 Opening Remarks and Overview of Workshop
    by Tan Tin Wee, APBioNet Secretariat and Project Co-Leader
    
    
  • 1340 The BioBox Initiative: Bio-ClusterGrid
    by Maddie Wong, Deepak Jeevankumar, Gilbert Thomas and Simon See, Asia Pacific Science and Technology Center (APSTC), Sun Microsystems | ppt |
    
    
  • 1350 BioCluster Grid tutorial
    by Maddie Wong, Sun APSTC
    BioClusterGrid Web Interface (user1 password)
    | blasttutorial.doc | clustaltutorial.doc | clustalseq.txt
    | APSTC BioBox Project | Download site |
    
    
  • 1415 Introduction to APBioBox and Hands-on installation of APBioBox, EMBOSS-GUI
    by Ong Guan Sin, APBioBox project consultant and Tan Tin Wee, National University of Singapore Requirement: Redhat version 9 (server installation) | ppt |
    
    
  • 1425 Introduction to KOOPlatform and LiveBase demo
    by Vinodh Rajesh, KOOPrime Pte Ltd
    Requirement: JDK1.4.1 and Java Web Start running on JRE 1.4.1 installed as a pre-requisite. Note that JDK 1.4.1 and JWS are bundled in and used by APBioBox directly.
    | LiveBase ppt | KOOPLite demo doc |
    | To start KOOPLite, click http://exon.bic.nus.edu.sg:9090/koopclient/index.html |
    
    
  • 1430 KOOPLite Practice
    
    • Requisite requirements
      For the hands-on, the students must have full internet access. Their machines must be installed with JDK1.4.1 and Java Web Start running on 1.4.1. They must be able to access the following url for J2RE_1.4.1_07 for Windows Ftp to ftp://exon.bic.nus.edu.sg in the JSE sub directory. If they have 1.4.2, the KOOPClient wont be started because of some security certificate issues.

    • To test installed KOOPLite:
      1. Execute the service notice:,   /opt/jboss-3.0.6_tomcat-4.1.18/bin/run.sh
      2. In the web browser, goto this url,
         http://exon.bic.nus.edu.sg:9090/webkoop/jsp/login.jsp
      3. use, 'admin' and 'admin' for login.
      4. In the page, click on the 'Start Server' button 
         in the left frame.
      5. If koopserver started successfully, a message will appear in 
         the right frame.
      6. then start the koopdaemon, by executing,
         /usr/java/javaws/javaws/javaws http://exon.bic.nus.edu.sg:9090/koopclient/launch_daemon.jnlp
      7  from the command line in the exon server terminal.
      

  • 1500 End of Workshop
    
  
  
  
• Additional Workshop Materials
  • EMBOSS-GUI developed by Luke McCarthy at Plant Biotechnology Institute, Canada. | Original Download Site | tar.gz copy |
  • CGI perl module (required by EMBOSS-GUI)
  • Mailer perl module(required by EMBOSS-GUI)
  
  
  
• Discussion Material and Links
  • Alchemi
    Those of you who are interested in building a PC/Desktop Grid using Windows, you may want to explore the use of Raj Buyya's .NET based Grid system. For more info on what it is, how to deploy it, and use it, please browse http://www.alchemi.net
    
    
  • Gridbus Broker - has been integrated to work with Alchemi in addition to Unix-class resources running Globus. You will be able to make use of both of them at the same time. More about the broker can be found at Gridbus Broker website
  
  
  
• Participants and Trainers

  Participants
  ------------
  M.Ivanou			Institute for Infocomm Research
  Goh Kiah Mok		Singapore Institute of Manufacturing Technology
  Donny Soh Cheng Lock	SMA-NUS
  Zhang Xinhuai		Computer Centre, NUS
  Feng Yuhong		SCE, NTU
  Xiong Xuejian		SMA, NUS
  Yuan Guojun		NUS
  Vinisha Khemani Kanjilal	Lilly Systems Biology
  Markus Wenk		National University of Singapore
  wang donghong		data storage institute
  Teddy Sulimin		Nanyang Polytechnic
  Atif Shahab		Bioinformatics Institute
  David Verde Sanchez	Biotech Instrumentation consulting
  Adrian Png		Nanyang Polytechnic
  Darran Nathan		DSP Technology Centre, NgeeAnn Polytechnic
  Chan Hoong Maeng		Institute of High Performance Computing
  Yeo Wee Kiang		IMCB
  JIANG Beibei		Singapore Computer Systems
  Napat Chalakornkosol	Singapore Computer System
  Fan Siyu			NUS
  Leong Hon Wai		National University of Singapore, Dept of Computer Science
  Choo Thong Tiong		NTU (student)
  Abel Ang			EDB
  Sebastian Ho		Bioinformatics Institute
  yong how choong		BII
  Liu Xiaoxing		Bioinformatics Institute
  S P T KRISHNAN		INSTITUTE FOR INFOCOMM RESEARCH
  LAI Loong Fong		Bioinformatics Institute
  Nigel Teow		BII
  Mark De Silva		BioInformatics Center, National University of Singapore
  Lim Kuan Siong		BioInformatics Center, National University of Singapore
  Lim Yun Ping		BII
  Aamer Aziz		Bioinformatics Institute
  
  
  Trainers
  --------
  Maddie Jingtheng.Wong, Sun APSTC
  Gilbert Thomas, Sun APSTC
  Deepak Jeevankumar, Sun Microsystems
  Simon.See, Sun Microsystems
  Ong Guan Sin, SCS Ltd
  Teo Cheng Hon, SCS Ltd
  Jon Lau, National Grid Computing Office
  Kao Feng, KOOPrime author and architect
  Vinodh,  KOOPrime Pte Ltd
  Victor Tong, NUS
  Tan Tin Wee, NUS
  

• Sponsors
  • International Development Research Centre - PAN R&D Grant
  • Agency for Science, Technology and Research (A*STAR) Singapore
  • Institute for InfoComm Research (I2R) Singapore
  • National Grid Office, Singapore
  • Sun Microsystems
  • KOOPrime Pte Ltd
  • SCS Ltd
• Endorsed by
  • Asia Pacific Bioinformatics Network