Course Information:

Course Description: The objective of this course is to provide a hands-on, self-directed experience dealing with biological data and integrating it to produce software and analyses that are of use to biologists. Students will be given a project and asked to design a solution using a combination of existing tools and their own developed software.

Instructors:

Joel McManus
mcmanus@andrew.cmu.edu
Office: MI 255,
Phone: 412-268-9407

Carl Kingsford
carlk@cs.cmu.edu
Office: GHC 7705
Office Hours: 3pm-4:30pm, Mondays in GHC 7705.

Syllabus: Here is a detailed class syllabus.

Project: Here is a description of the class project.

Announcements

• Second reading assignment:
  1. http://www.sciencemag.org/content/331/6016/430.short
• First progress report is due March 25. It should be at least 2 pages and include 4 sections: (1) brief description of the project in your own words; (2) list of resources and papers that are relevant and that you will investigate more; (3) a list of questions about the project that you could not answer during your research; and (4) assignment of roles to each team member.
• First reading assignment:
  1. Hiller NL, Ahmed A, Powell E, Martin DP, Eutsey R, et al. (2010) Generation of Genic Diversity among Streptococcus pneumoniae Strains via Horizontal Gene Transfer during a Chronic Polyclonal Pediatric Infection. PLoS Pathog 6(9): e1001108. doi:10.1371/journal.ppat.1001108
  2. Hiller NL, Eutsey RA, Powell E, Earl JP, Janto B, et al. (2011) Differences in Genotype and Virulence among Four Multidrug-Resistant Streptococcus pneumoniae Isolates Belonging to the PMEN1 Clone. PLoS ONE 6(12): e28850. doi:10.1371/journal.pone.0028850