Bioinformatics! ….and some more PCR

I hope that everyone saw and thoroughly enjoyed the PCR Song from my previous post. This comic expresses perfectly how I feel today.

python

This comic is particularly relevant because I am pretty sure that I learned more about Bioinformatics, python, and coding in general from this morning’s computer lab session than over two years of trying to teach myself enough coding to get data through QIIME (Quantitative Insights into Microbial Ecology). So the progress that we made today did indeed feel like flying. I really enjoyed Ipython. I have already installed it on my computer and will be looking into how to incorporate QIIME. I am also really excited to learn how to incorporate R into IPython. A shout out to Lauren’s most recent post: Rosalind.info is awesome! I have already completed several exercises so I feel more prepared for tomorrow. I couldn’t figure out how to access Maxene from my personal computer I don’t have the ipythen notebook to post here.

Update on the Laby Project

So Casey, Ruth, and I tried two DNA extractions on the same water samples. One was the DNeasy kit, the reliable, but somewhat limited (in terms of # of samples we can process) method. The other was the boil prep method for Colony PCR. This simply utilizes osmonic pressure and heat to lyse cells and inactivate DNases. For those of you who think I’m crazy, here is the first report of colony PCR (back in 1989). colonyPCR If this works (which it should because there is Laby on all the samples processed) then the boil prep is a cheap, quick, and limitless alternative to the column based kits. We sot up the same PCR reaction and thermocycler conditions as my previous post. Stay tuned for the results.2014-08-04 19.31.40

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