Simon Fraser University
Engaging the World

Course Outlines

Fall 2019 - CMPT 711 G100

Bioinformatics Algorithms (3)

Class Number: 9017

Delivery Method: In Person

Overview

  • Course Times + Location:

    Sep 3 – Dec 2, 2019: Tue, 2:30–4:20 p.m.
    Burnaby

    Sep 3 – Dec 2, 2019: Thu, 2:30–3:20 p.m.
    Burnaby

  • Exam Times + Location:

    Dec 12, 2019
    Thu, 3:30–6:30 p.m.
    Burnaby

Description

CALENDAR DESCRIPTION:

Fundamental algorithmic techniques used to solve computational problems encountered in molecular biology. This area is usually referred to as Bioinformatics or Computational Biology. Students who have taken CMPT 881 (Bioinformatics) in 2007 or earlier may not take CMPT 711 for further credit.

COURSE DETAILS:

This is a course on fundamental algorithmic techniques used to solve computational problems encountered in molecular biology. The course will investigate both traditional deterministic algorithms such as dynamic programming as well as machine learning and AI methods in Computational Biology. We will focus on practical algorithmic solutions as well as theoretical challenges. The course will have a project based on student's choice. The course satisfies the "Area I - Theory" requirement.

Topics

  • Molecular biology basics
  • Public Databases and Tools
  • Sequence Analysis (local and global alignments)
  • Multiple Sequence Alignments
  • Dynamic Programming
  • Markov Chains and Hidden Markov Models (HMMs)
  • Sequence Similarity Search
  • RNA secondary Structure Prediction
  • Thermodynamic Models
  • Machine Learning: Evolutionary Computation, Neural Networks

Grading

NOTES:

Students must attain an overall passing grade on the weighted average of exams in the course in order to obtain a clear pass (C- or better). Details will be discussed in the first week of classes. There will be assignments and a project and also a midterm exam.

Materials

REQUIRED READING:

An Introduction to Bioinformatics Algorithms
Neil Jones and Pavel Pevzner
MIT Press
2004
ISBN: 9780262101066

RECOMMENDED READING:

Bioinformatics: The Machine Learning Approach
Pierre Baldi, Sren Brunak
MIT Press
2001
ISBN: 9780262025065

Algorithms on Strings, Trees, and Sequences
Dan Gusfield
Cambridge University Press
1997
ISBN: 9780521585194

Biological Sequence Analysis: Probabilistic Models of Proteins & Nucleic acids
R. Durbin, S. Eddy, A. Krogh, G. Mitchison
Cambridge University Press
1998
ISBN: 9780521629713

Graduate Studies Notes:

Important dates and deadlines for graduate students are found here: http://www.sfu.ca/dean-gradstudies/current/important_dates/guidelines.html. The deadline to drop a course with a 100% refund is the end of week 2. The deadline to drop with no notation on your transcript is the end of week 3.

Registrar Notes:

SFU’s Academic Integrity web site http://www.sfu.ca/students/academicintegrity.html is filled with information on what is meant by academic dishonesty, where you can find resources to help with your studies and the consequences of cheating.  Check out the site for more information and videos that help explain the issues in plain English.

Each student is responsible for his or her conduct as it affects the University community.  Academic dishonesty, in whatever form, is ultimately destructive of the values of the University. Furthermore, it is unfair and discouraging to the majority of students who pursue their studies honestly. Scholarly integrity is required of all members of the University. http://www.sfu.ca/policies/gazette/student/s10-01.html

ACADEMIC INTEGRITY: YOUR WORK, YOUR SUCCESS