James and the Giant Corn Genetics: Studying the Source Code of Nature

December 10, 2008

New Blast Server

Filed under: Uncategorized — James @ 10:44 am

Visited a delicious burger restaurant in Berkeley today after class. They server beef, veggie, chicken and turkey burgers… to which my reaction was “No pork?” Seriously though it was very tasty, I was pleasant surprised.

Life is still really busy. I went in both days of this weekend to keep running reactions. I’ve also set up a local blast server for the lab.* I got to build the computer from left over parts from two computers that another grad student had inherited when a friend upgraded his LAN gaming set up. So the new lab blast server lives in a giant gaming case, with clear plastic sides and glowing blue lights.

After mixing and matching pieces it was just a matter of installing Ubuntu, setting up the webserver and blast server programs, and installing databases like the brachypodium and maize genomes. I’ve been accumulating this skill set for two and a half years, since Monty first showed me how to build a desktop computer and I got a summer job that got be started using the command line a perl scripts. It was really fun to put all the pieces together and go from two broken computers and an internet connection to a functioning piece of equipment of measurable benefit for the whole lab.

*Some context, BLAST is a program used to search for other genes related to the one you’re interested in, which can help apply knowledge gained from studying one organism to others. Along with PCR probably the most universal mainstays of a modern molecular biology lab.

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