Archive for February 2nd, 2009

Looking for genome assembly papers

Monday, February 2nd, 2009

I’m starting a journal club for the computer scientists at BiRC.  Since it is me starting it up, I have egoistically chosen a subject I personally would like to learn more about.  Algorithms for Next Generation Sequencing assembly.

Now I don’t even know much about the “plain old” sequence assembly algorithms, so I want to start out with a few papers on that and then move to newer algorithms.

The only problem is that I don’t know which papers are important and which are not.

So if anyone have any ideas, please please let me know!

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Python threads

Monday, February 2nd, 2009

Jesse Noller has an excellent post on Python Threads and the Global Interpreter Lock that is well worth a read.

I, in particular, liked the use of decorators to get the “synchronized” feature known from Java and the long discussion about the GIL.

I haven’t used threads much in my own Python code — I usually split my scripts in separate processes to parallelise them on our cluster — so there were a lot in this post I didn’t know about.

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