Simon Fraser University
Engaging the World

Course Outlines

Fall 2020 - CMPT 711 G100

Bioinformatics Algorithms (3)

Class Number: 6665

Delivery Method: In Person

Overview

  • Course Times + Location:

    Sep 9 – Dec 8, 2020: Mon, 4:30–5:20 p.m.
    Burnaby

    Sep 9 – Dec 8, 2020: Wed, Fri, 4:30–5:20 p.m.
    Burnaby

  • Exam Times + Location:

    Dec 11, 2020
    Fri, 7:00–10:00 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 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. Students need to have access to a computer, web-cam, and mic and a sufficiently stable internet connection as most content will be delivered online. Lectures will be given in live mode with an opportunity for students to interact. Lectures will also be recorded and posted.

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

  • There may be assignments, a midterm, a project and/or a final exam. Details will be discussed in class in the first week of classes. 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).

Materials

MATERIALS + SUPPLIES:

Required Books

  • An Introduction to Bioinformatics Algorithms, Neil Jones and Pavel Pevzner, MIT Press, 2004, 9780262101066

RECOMMENDED READING:

  • Biological Sequence Analysis: Probabilistic Models of Proteins & Nucleic acids, R. Durbin, S. Eddy, A. Krogh, G. Mitchison, Cambridge University Press, 1998, 9780521629713
  • Bioinformatics: The Machine Learning Approach, Pierre Baldi, Sren Brunak, MIT Press, 2001, 9780262025065
  • Algorithms on Strings, Trees, and Sequences, Dan Gusfield, Cambridge University Press, 1997, 9780521585194

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:

ACADEMIC INTEGRITY: YOUR WORK, YOUR SUCCESS

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

TEACHING AT SFU IN FALL 2020

Teaching at SFU in fall 2020 will be conducted primarily through remote methods. There will be in-person course components in a few exceptional cases where this is fundamental to the educational goals of the course. Such course components will be clearly identified at registration, as will course components that will be “live” (synchronous) vs. at your own pace (asynchronous). Enrollment acknowledges that remote study may entail different modes of learning, interaction with your instructor, and ways of getting feedback on your work than may be the case for in-person classes. To ensure you can access all course materials, we recommend you have access to a computer with a microphone and camera, and the internet. In some cases your instructor may use Zoom or other means requiring a camera and microphone to invigilate exams. If proctoring software will be used, this will be confirmed in the first week of class.

Students with hidden or visible disabilities who believe they may need class or exam accommodations, including in the current context of remote learning, are encouraged to register with the SFU Centre for Accessible Learning (caladmin@sfu.ca or 778-782-3112).