1. Introduction; molecular biology review
2. Overview of databases and tools
3. Basic scripting: files, variables, parsing
4. Intermediate scripting: high-level data structures
5. Advanced scripting: objects, references, libraries
6. RNA logic and virus design
7. Sequence analysis pt 1: dynamic programming
8. Sequence analysis pt 2: alignment and search tools
9. Algorithmic complexity
10. Probability and statistics
11. Information theory and bioinformatics
12. Multiple alignment and phylogeny
13. Pathways and systems
14. Special topics
15. Review

• Key dates
  • Academic calendar (Fall 2009)
  • Exams:
    • Midterm 1: Wednesday September 30, 3:10-4pm
    • Midterm 2: Wednesday November 18, 3:10-4pm
    • Take-home final
  • Final project deadlines: see project page

• Grading scheme
  • 40% homework assignments
  • 25% midterm exams
  • 35% final project

• Extensions/Alternate Exam Dates
  • Requests for extensions on homework due dates must be submitted to Ian Holmes via email at least 2 days before homework due date, clearly stating reason(s) for request.
  • Please plan to attend the scheduled exam/presentation times. Requests for alternate exam/presentation dates must be submitted to Ian Holmes via email as soon as possible, clearly stating reason(s) for request. An alternate date request is only likely to be granted under extreme circumstances (family emergencies, major illness, etc.)
  • Conflicting commitments on other courses will not usually be considered adequate reason to moving exams or homework deadlines unless the conflict is experienced by a majority of the class.
  • Every year several requests failing to meet the above criteria are declined -- please do not invite mutual disillusion by asking for an exception.

• Teamwork
  • We want to encourage you to work together, so for regular homework assignments, you may submit jointly with up to one other student as long as you identify who it was you worked with. However, we also want to encourage mixing, so you can contribute no more than three homework assignments with any one partner. After that you will have to rotate with someone else.

Tasks for first week

Register a student account on biowiki.org at the following URL:

http://biowiki.org/view/Teaching/StudentRegistration

Once registered, email your account details to bioe131reg@postbox.biowiki.org so that your account can be authorized to add links and attachments to the wiki (this will be necessary for subsequent homework assignments).

You should also pick up your DECF account details; either in lab, or directly from the DECF lab assistant whose schedule can be found at

http://www.decf.berkeley.edu/labasst.html