Progress of the Project
It is challenging and interesting that my three supervisors have different ideas about the project. Wilfred is interested in using Nimrod's meta-scheduling capability. Ilkay wants to create a work flow that can be extended later to include parameter sweep. Colin suggested me to extend the Opal actor to use GridFileTokens. While those ideas add an extra level of complexity to the project, it helps me view the project from different perspectives because my supervisors came up with the idea based on their expertise.
In week 2 meeting, it has been finally agreed that we will follow Ilkay's suggestion to construct a work flow first. Thanks to Jianwu and Jane's assistance, I have two candidate work flows at the moment:
This work flow submits DNA or protein sequences to MEME. MEME will analyze your sequences for similarities among them and produce a description for each pattern/motif it discovers. The analysis results is displayed in a web browser. The work flow is retrieved from https://code.kepler-project.org/code/kepler/trunk/workflows/meme-opal/ To view a sample output, visit http://ws.nbcr.net/app1295390134402/. The required parameters to be specified in this work flow include the occurrences of a single motif, maximum and minimum width of motif, maximum number of motif. There are also many optional parameters. Those parameters can be used later to implement parameter sweep.
The original work flow use MEME 4.1.0 web service which is no longer supported by NBCR. Therefore, I modified the work flow to use MEME 4.5.0. The problem with the work flow is that when I save the modified work flow, the work flow cannot find At.fa sequence file at execution time. I plan to consult Jianwu again to fix this problem.
This work flow perform a PDB to PQR file format conversion using NBCR remote computation capabilities. It runs smoothly. Visit http://ws.nbcr.net/app1295392505925/ to view the results. However, I'm not sure if it make sense to do parameter sweep. I need to talk to Wilfred to find out if the parameter sweep can help solve scientific problem.
Entertainment
We rent a car and visited Las Vegas during the long weekends. We pretty much went to every big casino. Unfortunately, Wai Keung and Geoff lost around $100 in gambling. The buildings and scenery in downtown are more attractive to me than gambling.
Bad News
My dad told me that my mum had a big surgery. The surgeon opened my mum's belly and removed four tumors. I hope my mum will recover soon.
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