Continuing with Unix/Programming after the course


(The usb memory stick has limited lifespan. With consistent use, it will satrt failing at some point. BACKUP your work/files.)

Windows



  • ocf: http://www.ocf.berkeley.edu/
    (free web hosting)
    downsides: space limit of 400MB, must write scripts in-terminal, or copy from your machine

  • cygwin http://www.cygwin.com/
    Best for connecting to remote unix machines
    Great for writing perl scripts, using almost full unix functionality
    downsides: installing bioinformatics programs like BLAST is a real challenge

    • Choose the following packages before installing:
      • net: openssh, curl
      • perl: perl, perl_manpages
      • X11: X-startup-scripts
      • Web: wget
      • Database: postgresql, postgresql-doc, postgresql-plperl
      • Editors: nedit, xemacs, xemacs-sumo
  • (type "startx" after starting cygwin to enable non-terminal programs)


MAC

  • There's not much to do - you already have Unix.
  • While the standard terminal will work for many tasks, a much better terminal is X11. X11 let's you use Unix-based programs that open other windows: http://www.apple.com/macosx/features/x11/
  • X11 as well as a bunch of other items that will make your Mac more like a standard Linux or Unix machine are available in the Xcode bundle on your Install Discs that came with your machine: http://developer.apple.com/tools/xcode/
  • Be warned that not everything works perfectly on a Mac. Usually if you google a program you want to add, you can find someone that has gotten it to work or a consensus that no one can.

Linux

  • LiveCD+usb
There is software on the CD
http://intro-prog-bioinfo-2007-ucb.wikispaces.com/LiveCD%20software%20list

Exercises


1. Follow the final instructions on the project page. Map the conservation of the yeast CDC42 onto the structure using pymol. If you have time, you may also consider rendering the other proteins' conservation onto the structure.