UCSF Jain Laboratory

BMI-203: Biocomputing Algorithms, Winter 2010 - 3 units
Class: Tuesdays and Thursdays 3-5pm
Room: Byers Hall Room 215 (Mission Bay campus)

Week Date Topic Lecturer Assignment

1 Jan 5 Course overview
Complexity theory and Sorting Jain 1

1 Jan 7 Paper presentation TBD -

2 Jan 12 Graph theory and Searching Jain -

2 Jan 14 Paper presentation Student -

3 Jan 19 Dynamic Programming Jain -

3 Jan 21 Paper presentation Student -

4 Jan 26 Clustering Pegg 2

4 Jan 28 Paper presentation Student -

5 Feb 2 Optimization I: Overview and Global Methods Jain -

5 Feb 4 Paper presentation Student -

6 Feb 9 Optimization II: Local Methods Jain 3

6 Feb 11 No presentation. - -

7 Feb 16 Parameter Estimation and Machine Learning Jain -

7 Feb 18 Paper presentation Student Final Project

8 Feb 23 No Lecture - -

8 Feb 25 Paper presentation Student -

9 March 2 Probabilistic models I: Hidden Markov Models Pegg -

9 March 4 Paper presentation Student -

10 March 9 Probabilistic models II: Phylogenetic Trees and Matrices Pegg -

Final projects are due on Monday, March 8.
Homework assignments represent 40% of final course grade. They are due two weeks after being assigned (by midnight according to email timestamp).
Classroom participation represents 30%. This includes paper presentations, which will encompass both presentations of relevant published algorithmic research as well as presentations of the algortihmic components of students' proposal efforts within the broader iPQB program.
The final project represents 30%.