Simon Fraser University
Engaging the World

Course Outlines

Fall 2019 - CMPT 441 D100

Computational Biology (3)

Class Number: 9006

Delivery Method: In Person

Overview

  • Course Times + Location:

    Tu 2:30 PM – 4:20 PM
    RCB 8100, Burnaby

    Th 2:30 PM – 3:20 PM
    RCB 8100, Burnaby

  • Exam Times + Location:

    Dec 12, 2019
    3:30 PM – 6:30 PM
    WMC 3210, Burnaby

  • Prerequisites:

    CMPT 307.

Description

CALENDAR DESCRIPTION:

This course introduces students to the computing science principles underlying computational biology. The emphasis is on the design, analysis and implementation of computational techniques. Possible topics include algorithms for sequence alignment, database searching, gene finding, phylogeny and structure analysis. Students with credit for CMPT 341 may not take this course for further credit.

COURSE DETAILS:

This is an introductory 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.

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. Details will be discussed in class in the first week of classes.

Materials

REQUIRED READING:

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

RECOMMENDED READING:

  • Biological Sequence Analysis
  • Richard Durbin, Sean Eddy, Anders Krogh, Graeme Mitchison
  • Cambridge University Press
  • 1998

ISBN: 9780521629713

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

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