CSI 5126 (COMP 5108) Fall 2010 course description

CALENDAR DESCRIPTION:
CSI 5126. Algorithms in bioinformatics (3 hs of lecture per week, 3 credits).
Fundamental mathematical and algorithmic concepts underlying computational molecular biology; physical and genetic mapping, sequence analysis (including alignment and probabilistic models), genomic rearrangements, phylogenetic inference, computational proteomics and systemic modeling of the whole cell.
Prerequisite: CSI 3105, COMP 3804 or equivalent.
WEB PAGE: http://www.site.uottawa.ca/~lucia/courses/5126-10/
PROFESSOR: Lucia Moura
tel: 562-5800 ext. 6678
email: lucia@site.uottawa.ca
OFFICE HOURS: Office: SITE 5-027 
Wednesdays 1:30-2:30, Fridays 2:30-3:30 or by appointment.
LECTURES: Tuesday 11:30-1:00 and Friday 1:00-2:30 (room BRS 204, Brooks Residence).  
TEXTBOOK: Wing-Kin SUNG, Algorithms in Bioinformatics, CRC Press, 2009. ISBN 978-1-4200-7033-0.
The textbook is required!
OTHER
REFERENCES:		 Check references (recommended textbooks, essential cell biology and other textbooks)
in Marcel Turcotte's page for previous offerings of this course.
COURSE
OBJECTIVES:
  • To introduce the main problems arising in bioinformatics today for a student in computer science/mathematical sciences.
  • To gain an in-depth understanding of algorithmic techniques applied in bioinformatics.
    • COURSE OUTLINE:
    (tentative)
    1. Introduction to Molecular Biology (chapter 1)
    2. Sequence Similarity (chapter 2)
    3. Suffix trees and related data structures (chapter 3)
    4. Genome Alignment (chapter 4)
    5. Multiple sequence alignment (chapter 6)
    6. Phylogeny Reconstruction (chapter 7)
    7. Genome Rearrangement (chapter 9)
    8. Other topics:
      RNA secondary structure prediction (guest lecture);
      other topics/guest lectures TBA
    MARKING SCHEME: 45% Assignments average = 3 assignments at 15% each;
    only if full presence to all student presentations and guest lectures;
    otherwise will take MINIMUM OF:
  • assignment average (45%)
  • assignment average (35%) + presence "score" in above lectures (10%)
    15% Review and oral presentation of a scientific publication (list of articles provided)
    40% Project = 5% project proposal (PP), 10% project talk (PT), 25% project report (PR) (topic chosen by student)
    • IMPORTANT
    DATES:

    		weight: due date: (tentative)
    Assignment 1 15%  Oct 5
    Assignment 2 15%  Oct 19-22
    Paper Review and Presentation 15%  Nov 2,5
    Project Proposal 5%  Nov 12
    Assignment 3 15%  Nov 30
    Project Talk 10%  Dec 7
    Project Report 25%  Dec ? TBA

    Dates from the Academic Calendar:
    First lecture: September 10 (Fri)
    Study break: October 24-30
    Last date to drop: Nov 5
    Last lecture: Dec 7 (Tues)