These are materials for the 2010 BEACON course, CSE 891 s002: Computational Science for Evolutionary Biologists.
Rather than developing a whole new site containing a lot of overlapping material, we’ll be integrating some BEACON material into the ANGUS site.
(Sep 10th, 2010)
In class, we worked through Starting your cloud system and Building and installing Avida.
You may find the Amazon Web Services cheat sheet useful later on.
(Sep 17th, 2010)
Just a reminder – you can always Google it, and the worst that will happen is you lose some data (which you can cleverly save by transferring it to your laptop, if it’s small enough!)
In class, we’ll work through the following tutorials:
Running jobs while you sleep: the ‘screen’ section of UNIX Cheat Sheet
- Transferring files:
- Windows: the Notepad++ and WinSCP sections of Using SSH/SCP on Windows
- Mac OS X: Using SSH/SCP on Mac OS X in the Terminal app
and finally we’ll go through Running Avida longer.
If you’re intrigued by UNIX and want to know more, you might want to check out this tutorial http://www.ee.surrey.ac.uk/Teaching/Unix/ .
Software Carpentry: A detailed video screencast introduction to the UNIX shell is available here.
See running-serial-transfers and transferring-files.
See mutation-analysis.
See Trying out mapping – using bowtie to map short reads to the Campylobacter genome: