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Week 9
Aug 5 - Aug 11
On returning I had to shift to a different room in Taylor Place. Students were moving in for the fall semester and so they had to move us to a suite in another tower. Skatje had already moved out her stuff. The suite was really big and we had our separate rooms with a common space. It was awesome. I missed rooming with Skatje though. She's a great roommate and friend and I actually don't like living alone all that much. Mark and Melissa had left Taylor space and moved into their own apartments. I knew no one in the building now. Gazi and Fabian were no longer around in the lab. Fabian was taking a course elsewhere. Gazi had gone to New Zealand to visit his family. Some of the other people I had met in the bioinformatics building - Chris, Aaron, Gatha weren't there either. Gatha was working from home while Chris and Aaron had graduated.
I met Professor Gonzalez to discuss what we may do next. We decided to try and use the GeneRanker plugin for cytoscape and see whether that gave different results. Also we planned on making all that I've been doing till now automated. I was excited and looked forward to writing codes. But it wasn't that easy. First of all the GeneRanker plugin refused to run on Cytoscape because some files were missing. So I got those files from Fabian and finally got it running. Secondly, GeneRanker is intended to only rank genes associated with diseases. It can be used to rank genes for ADRs since most ADRs are some form of disease. I was able to manipulate the GeneRanker available online to rank genes for drugs because it also allows you to input the seed genes yourself but this was not possible with the GeneRanker plugin for Cytoscape. So I had to upload the drug-gene network as a file into Cytoscape to compare the drug-gene network with the ADR-gene network. It turned out that when comparing the gene networks cytoscape also merely lists the genes present in the overlap between the two networks. So the results did not vary.
I didn't do anything much over the weekend. Skatje and I checked out a Vietnamese restaurant in Mill's Avenue. Mill's Avenue is a nice place in Arizona. It's always very busy and has tons of different restaurants. This was the first time I tasted Vietnamese food. It was awesome!
The following week I tried looking through the GeneRanker code and didn't understand a thing. It had no comments. My plea to everyone - please, please write good documentation for your code! It makes a huge difference!
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