Simon Fraser University
Engaging the World

Course Outlines

Fall 2018 - CMPT 441 D100

Computational Biology (3)

Class Number: 8416

Delivery Method: In Person

Overview

  • Course Times + Location:

    Sep 4 – Dec 3, 2018: Mon, Wed, Fri, 9:30–10:20 a.m.
    Burnaby

  • Exam Times + Location:

    Dec 12, 2018
    Wed, 12:00–3:00 p.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:

 

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 present a sampling of applications to the analysis of metabolites, proteins, genes, and their interactions. 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.

Topics

  • Sequence alignment, global and local
  • Phylogenetics - inferring evolutionary trees
  • RNA secondary structure prediction
  • Biological networks analysis

Grading

NOTES:

Option 1: 10% participation, 30% assignments (best 3 out of 4), 20% midterm, 40% final exam Option 2: 100% final exam.
While I highly recommend option 1, you will automatically get the higher of the two grades.

Materials

RECOMMENDED READING:

  • An Introduction to Bioinformatics Algorithms
  • Neil Jones, Pavel Pevzner
  • MIT Press
  • 2004

ISBN: 9780262101066

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

ISBN: 9780521629713

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