CS329E Fall 2006 Dr. David Kincaid

# Welcome CS329E Students Elements of Algorithms in Bio-Informatics Fall 2006 Dr. David Kincaid

Dr. David R. Kincaid, PAI 5.48, Tel: 471-9783, Fax: 471-8885
Office Hours: immediately after class in RLM 13.158
or via email kincaid@cs.utexas.edu or by appointment.
TA: Nathan Paczan Office Hours: MW 2-3pm, PAI 5.38 (Elements Lab) or via email npaczan@cs.utexas.edu
Class Syllabus

Lectures:

Assignments:
• HW1 Due: 09/12 (Tue); Can use any word processing system: Word, LaTeX, etc.
• CP1 (Due: 9/21) Fibonacci Algorithms
• HW2 (Due: 9/28) Chapter 2, Problems 2.2, 2.3, 2.11, 2.15, 2.16 <- Assume n is less than or equal to 10 and the size of each of the two new piles must be equal or approximately equal and must add up to the size of the original big pile. Extra Credit: 2.16 as given in textbook.
• CP2 (Due: 10/17) Cp2.ps, Cp2.pdf
• HW3 (Due: 10/26) Chapter 8, Problems 8.1, 8.2, 8.3, 8.6, 8.9
• CP3 (Due: 11/5) Pattern Matching and Searching: CP3.ps, CP3.pdf
• HW4 (Due: 11/9) 4.2,4.4,4.5,6.1.7.1
• Extra Credit (Due: 12/12): extra.ps, extra.pdf
Examinations:
• Exam I (10/5)
• Exam II (11/14)
• Final Exam (12/14) WEL 3.422
General questions on material covered in textbook and lectures wrt concepts, algorithms, and problems. Objective Format: Fill-in the blank, True/False, Short answers.

Miscellaneous Information:
Special Office Hours, Monday (12/11) and Tuesday (12/12), 2-3pm, Dr. Kincaid, PAI 5.48
Review Session: Nathan Paczan, Elements Lab, Monday (12/11), 7pm.
• No Class Tuesday 11/21
• Student Presentations:
• Tuesday (11/28)
• Tara Long --- Randomized Algorithms: Gibbs Sampling, Random Projects
• Thursday (11/30)
• Layla Young --- Protein ID (Sec. 8.10-8.15)
• John Leavitt --- Hidden Markoff Methods
• Tuesday (12/5)
• Kristin Schroter --- Genes and DNA (3.3-3.6, 3.8)
• Erika Kase --- Combinatorial Pattern Matching
• Ajay Mody --- Combinatorial Problems
• Santosh Dawson --- Randomized Algorithms
• Thursday (12/7)
• Beatrie Santillan --- Gibbs Sampling
• David Rushworth --- Neutral Networks
• Marcus Reid --- Trees and clustering (Chp 10)
• Todd Gillespie ---
• Louis Guzick ---

08 Dec 06