HW 1B Thread

Please put questions regarding HW1B in this thread.

1. Note: minor update of HW1b. I added a link to Robert Edgar's review of multiple sequence alignment in Current Opinion in Structural Biology, and clarified that you also want to include the first row and column for the optimal score matrix.
   

HW 1A Thread

Please put questions regarding HW1A in the comments to this thread. If you sign up for blogger with your leland username it will be easier for me to put a name to your comments. Below are some questions I received by email which I anticipate will be common:

1. The version of Unix I have is Cygwin. Is that compatible?
   
   You can probably get through the class with Cygwin. I've used it in the past in a pinch, when I needed to use some Windows specific applications.
   
   However, if possible, I really do recommend getting accustomed to running Linux on its own. Nothing can really substitute for learning some system administration skills and the architecture of a Unix box. Unix, like C, is one of the few things that you can count on to be useful in computer science even 20 years from now. It's as close to a fundamental as you can get outside of mathematics. Also, the ability to solve your own problems by Googling error messages is an invaluable skill for a researcher. Even if all you get out of the course is a familiarity with Unix, aside from the bioinformatics this is a very valuable skill in its own right; Cygwin won't totally develop these muscles.
   
   
2. What is the procedure for hd partitioning?
   
   If you have a new hard drive (which is probably the easiest and best way to install Linux) then during the installation procedure you can partition the drive. If you need to shrink your existing Windows partition to make room for Linux, see the following links:
   
   Shrinking Windows Partitions with Gnome Partition Editor
   Partitioning Overview
   
   

Stat 366 FAQ

All right, this is the first post on the Stat 366 blog. You should use this blog for the primary communication with myself and the TAs; it's fine to use email when necessary, but for questions in which your fellow students would benefit from the answer, the blog is best.


1. Units: There is no difference between the 2 and 3 unit options. The 2 unit option is mainly offered as a convenience for graduate students.

2. Books: The programming tools books will serve you well for at least the next 5 years in science, even if you don't decide to do bioinformatics. As for Jobling's book, it's the best thing out there and is well worth the purchase if you decide to work in the booming area of population genomics.

3. Comments: You will need to sign up for a Blogger account to leave comments. Please sign your comments with your leland username if this is not already taken as a Blogger username. If it is already taken, sign up for a close approximation.


Ok. In general, I will start one thread to unify questions on a HW. The next post will be for homework 1.