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

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

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.

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.

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.

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

Logging on to compgenomics SecureCRT or PuTTY or Cygwin Terminal

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.

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

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.

Final Output is a Pretty Picture This is the fourth year that this course is being offered. See: compgenomics.biology.gatech.edu and www.compgenomics2009/10.biology.gatech.edu 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