Simon Fraser University
Engaging the World

Course Outlines

Fall 2017 - CMPT 441 D100

Computational Biology (3)

Class Number: 7097

Delivery Method: In Person

Overview

  • Course Times + Location:

    Sep 5 – Dec 4, 2017: Mon, Wed, Fri, 9:30–10:20 a.m.
    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:

Please note - this course is cross-listed with CMPT 711

The goal of this course is to provide a solid foundation in the algorithmic techniques, such as dynamic programming, graph theory and probabilistic modelling, that computational biologists use on a daily basis, as well as to create exposure to the practice of computational biology through the analysis of a biological dataset. The course targets both graduate and advanced undergraduate students in computing science, molecular biology, biochemistry, biophysics, mathematics and biostatistics with minimal or no background in computational biology. However, a basic knowledge of algorithm design and analysis is required.

Topics

  • Sequence alignment: global, local and multiple alignment
  • Probabilistic models: hidden Markov models, stochastic context-free grammars
  • Secondary structure prediction: RNA and proteins
  • Phylogenetics: inferring and analyzing evolutionary trees

Grading

NOTES:

10% participation, 20% midterm, 30% assignments (best 3 out of 4), 40% team project. The team project will involve the analysis of a biological dataset provided by a life sciences faculty member. It will be evaluated via an oral presentation and a written report.

Materials

RECOMMENDED READING:

Biological Sequence Analysis
Richard Durbin, Sean Eddy, Anders Krogh, Graeme Mitchison
Cambridge University Press, 1998
ISBN: 9780521629713

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

Registrar Notes:

SFU’s Academic Integrity web site http://students.sfu.ca/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