BioWorldWideWorkFlow (bioWWWF)

The BioWorldWideWorkFlow uses the KOOPlatform software as the GUI frontend, the KOOPServer as the middleware scheduling server, and the KOOPDaemon as the remote server agent for executing applications called from the GUI and scheduled by the KOOPServer. KOOPrime is the spinoff company from the Bioinformatics Centre, National University of Singapore (NUS). KOOP technology was derived from the BIC research project with GlaxoWellcome and NSTB funding to BIC from 1997 to 2001. NUS maintains a license to run and operate the technology. The APBioGrid project provides additional layers of services which KOOP can call, and provides the interface with Globus Grid, BioCluster Grid and the APBioBox packages for rapid replication of applications and services.

Starting the KOOPserver logon exon as root cd /opt/jboss-3.0.6_tomcat-4.1.18/bin ./run.sh & to start jboss Java Bootstrap Environment Once the processes are successful started (check ps -ef), start web browser Go to http://exon.bic.nus.edu.sg:9090/webkoop/jsp/login.jsp When you see the page, key in admin as user name and admin as password. When you see the next page, "KOOPServer Web Administration", click button 'Start Server'. If you see the message 'KOOPServer started successfully' on the right panel, then the KOOPServer is started. Shutting down the KOOPserver Go to http://exon.bic.nus.edu.sg:9090/webkoop/jsp/login.jsp When you see the page, key in admin as user name and admin as password. When you see the next page "KOOPServer Web Administration", click button 'Start Server' should be greyed out, and the click button 'Shutdown Server' active. Select "Graceful" and click 'Shutdown Server' to shutdown the server gracefully. If you see the message 'Shutdown status: KOOPServer is successfully shutdown" the right panel, then the KOOPServer is successfully shutdown. To re-start server, proceed as in "Starting the KOOPserver" Occasionally, the server seems to hang, then login as root and kill all the java processes Starting the KOOPClient Click to this hyperlink to lauch the KOOPClient: http://exon.bic.nus.edu.sg:9090/koopclient/launch.jnlp Starting KOOPBox or KOOPDaemon from exon Execute /usr/java/javaws/javaws/javaws http://exon.bic.nus.edu.sg:9090/koopclient/launch.jnlp or launch_daemon.jnlp. Please note that KOOPBox will be shut down automatically once the ssh session is closed. A dedicated machine is needed to run koopdaemon at exon. Running KOOPDaemon on an Agent machine Login to Agent machine with an Xserver Start up webbrowser and go to http://exon.bic.nus.edu.sg:9090/koopclient/ to download KOOPDaemon. Please note Java Web Start is needed to run KOOPDaemon. A quirk of the software requires the session to be continuously running. To keep the KOOPDaemon alive, use console to start it, and keep the window alive. Once KOOPDaemon is running on your machine, it should be able to run KOOPServer-called applications on this KOOPDaemon machine.