Fall 2021 - CMPT 441 D100

Computational Biology (3)

Class Number: 4707

Delivery Method: In Person

Overview

  • Course Times + Location:

    Mo 12:30 PM – 1:20 PM
    AQ 3149, Burnaby

    Th 12:30 PM – 2:20 PM
    AQ 3149, Burnaby

  • Exam Times + Location:

    Dec 9, 2021
    3:30 PM – 6:30 PM
    WMC 3210, Burnaby

  • Prerequisites:

    CMPT 307 with a minimum grade of C-.

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 upper division 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. Please note that due to the evolving Covid 19 situation there may be required changes to the course delivery. As of May 26, 2021, the university has announced its plan for approximately 70-80% of teaching in person in Fall 2021. It has also stated that: "not all courses will be delivered in person. The fall will be a transitional term. Deans, supported by the work of chairs and directors, will make final decisions about whether courses will be taught remotely or in person." Please continue to check our course outline for further information. Should this course be taught remotely, students must have access to a computer with internet access, allowing the use of a conferencing system such as Zoom or BB Collaborate Ultra. Some components of the course will require synchronous (real-time) participation during the scheduled lecture and/or exam times. Visual proctoring may be required, subject to university approval.

COURSE-LEVEL EDUCATIONAL GOALS:

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:

There will be assignments, a midterm, and 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

REQUIRED READING:

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

ISBN: 9780262101066

RECOMMENDED READING:

  • Biological Sequence Analysis: Probabilistic Models of Proteins & Nucleic acids, R. Durbin, S. Eddy, A. Krogh, G. 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:

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 2021

Teaching at SFU in fall 2021 will involve primarily in-person instruction, with approximately 70 to 80 per cent of classes in person/on campus, with safety plans in place.  Whether your course will be in-person or through remote methods will be clearly identified in the schedule of classes.  You will also know at enrollment whether remote course components will be “live” (synchronous) or at your own pace (asynchronous).

Enrolling in a course acknowledges that you are able to attend in whatever format is required.  You should not enroll in a course that is in-person if you are not able to return to campus, and should be aware 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.

Students with hidden or visible disabilities who may need class or exam accommodations, including in the context of remote learning, are advised to register with the SFU Centre for Accessible Learning (caladmin@sfu.ca or 778-782-3112) as early as possible in order to prepare for the fall 2021 term.