MURPA-Lin Wei-Week 6

In this week, Wilfred agrees that we should build an OpalNimrod actor. The steps required to implement a prototype of the OpalNimrod actor:

1. Create a dummy xml file that stores application metadata.

2. Create a OpalNimrod actor based on the existing Opal actor.

3. The OpalNimrod actor uses Java Document Object Model to access the xml file.

4. Create a new user interface for the OpalNimrod to allow users to select an application name from a drop down list instead of defining the service URL. The drop down list is dynamically generated from the dummy xml file. After users select an application and click the commit button, the interface should display the input parameters for the selected application.

5. After users specify the parameter values and run the workflow, all the serviceURLs that run the application are stored in an array along with the serviceURL metadata. The array is passed to the Nimrod/K scheduler. The scheduler chooses a serviceURL based on the number of free CPUs.

6. At last, the input parameters are submitted to the chosen service URL.

The actor can be tested by changing the value of the number of free CPUs in the XML file and run a PDB2PQR workflow. ws.nbcr.net and kryptonite are the stable hosts that provide PDB2PQR web service. The Nimrod scheduler should choose between these two hosts.

Apart from creating an OpalNimrod actor, I will make a tutorial on how to run an Autodock virtual screening workflow on the NBCR wiki page because the new Opal plug-in will be released soon.