1. Introduction to Compgenomics
Andy Conley
January 19, 2011
MS, 2005
4th year PhD candidate in King's Lab
Working on N. meningitidis in collaboration with Leonard Mayer's lab

2. Introduction to Compgenomics
Collaboration
Wiki
Server
Final online product
Wiki
Documentation
Notes
Lectures
Anything else class-related
Server
Logging In
Programming
Genome Browser
Final deliverable

3. The Class Wiki
There is a Wiki for the class at: compgenomics2011.biology.gatech.edu
The Wiki shows the people and the groups there in.
For each group there is a page for a protocol.
We’ll use the Wiki to post presentations and information.

4. Wiki Accounts Right now, the Wiki is open. We want to close it.
Everybody needs to create an account on the Wiki.
Change your picture on the Wiki.

5. The Server
We have this nice Linux server that we have just for this class.
compgenomics.biology.gatech.edu
Everybody has an account on it.
You guys need to log in.
You guys need to know how to use the server.

6. compgenomics is our server
Class wiki
compgenomics2011.biology.gatech.edu
SSH (secureCRT)
Genome Browser
Website; view/edit documentation; useful for collaboration.
Command line commands
For publishing our data online for biologists to see

7. Logging on to compgenomics
SecureCRT or PuTTY or Cygwin
Terminal

8. Be Kind on compgenomics
Normally, you have your own computer
Here you are sharing, no sudo or anything
True Story: The first year, one group had all their stuff on 777 cause they were lazy. Some silly person deleted a bunch of it. Don’t be them.
Idea: Make a bin folder in your home directory, or make one for your group.

9. Collaboration on compgenomics
Lack of collaboration is the biggest complaint of employers for Georgia Tech graduates, undergrad at least
Collaboration is hard. It’s a lot easier to say “NO! MY CODE!”
That doesn’t work very well when you get to larger projects
I would (strongly) recommend you try a versioning utility: something like CVS or Subversion or Git. They all pretty much do the same thing
Browser group really has no choice in the matter

10. More Tips People from the fall are aware of my fondness of emacs
This is a much larger project than the scripts you wrote in there, and you may want to consider an IDE
I prefer Eclipse with the E.P.I.C. plugin. Eclipse has integrated CVS and Subversion.
Communicate with the groups upstream from you from day one. Like when I’m done talking.

11. Final Output is a Pretty Picture
This is the fourth year that this course is being offered.
See: compgenomics.biology.gatech.edu and
DO NOT COPY THEM
I have been involved with the class all three semesters.
In the end you will produce something like this.
Assembly, prediction, annotation, compgenomics, database groups