15 November 2013

teaching, DNA, jekyll, and pandoc

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Wed - Fri notes

2013-11-13

ApGenome

Aphaenogaster sample Genomic-tip DNA extraction day 2.

Nandrop results terrible!!! No idea why - saw beautiful strands of DNA at isopropanol precipitation stage and followed exact same protocol as previous extraction with Pogo after that.

1. Re-precipitated sample (500 ul) with 750 ul 70% EtOH. Centrifuged 10 min top speed. Air-dry. Re-hydrate in 200 ul Buffer AE and Nanodrop in morning.
2. I had saved Genomic-tip for this event. Added 1 ml Buffer QF. Precipitated in EtOH and centrifuged. Air-dry. Re-hydrate in 200 ul Buffer AE and Nanodrop in morning.

Website

While setting up jekyll for static website on xubuntu laptop, decided to write quick notes on install process:

Install jekyll, requires an up-to-date version of ruby

sudo apt-get install ruby1.9.1-dev
sudo gem install jekyll
# Need `pandoc-ruby` gem for pandoc compatability
sudo gem install pandoc-ruby

That’s it!

Clone the website and build or serve locally!

git clone https://github.com/johnstantongeddes/johnstantongeddes.org.git jekyll serve

Of course, this is for an install of my own website…a new website would require some more steps.

Added javascript to base html layout to allow mathjax in posts.

Computing

egglib python library for evolutionary genetics and genomics

2013-11-14

Prep for teaching BCOR 11 and Pop Gen classes.

2013-11-15

BCOR

Post-translation modification and kuru. Lecture slides here and case study here

Population Genetics

Research presentation.