S520, January 22

Here’s another edition of my notes from my S520 class.  (Sorry, I’m a little behind.) This time, I wrote all the notes in LaTeX, both for the challenge and for the practice.  Therefore, today’s entry is a PDF file, not a real blog post.  (Sorry.)  Here are the notes.  Let me know if you find any major errors.

Notes for January 22, 2010

By the way, I am still working on the RAMMCAP post I promised last time–it’s just turning out to be a lot longer than I’d originally intended.  I’ll probably break it up into multiple posts next week.

I’m back! (Part 2)

One other thing I’m going to try to use this blog for is to help me keep track of some of the tools I’m using for an RA project this year.  (“RA” in the “Research Assistant” sense, not the “Resident Advisor” sense.)  I’m studying metagenomics under Yuzhen Ye, specifically the automated functional prediction based on phylogenetic profiling (which is a fancy way of saying I want to figure out what the various pieces I’m working with do by comparing them with related genes in other organisms for which we know the function).

Needless to say, this new responsibility requires me to use a lot of tools that I’ve never heard of before, and I’ll feature some of them here, mainly so I can summarize the way they work and the way one uses them without having to refer back to the documention (which often is unclear, confusing, incomplete, or over-complicated).  Hopefully other people who come along after me can use these little tutorials and save themselves some time figuring things out.  I’m going to start out with a tool called RAMMCAP.