Simon Fraser University
Engaging the World

Course Outlines

Fall 2023 - CMPT 441 D100

Computational Biology (3)

Class Number: 6840

Delivery Method: In Person

Overview

  • Course Times + Location:

    Sep 6 – Dec 5, 2023: Mon, 2:30–4:20 p.m.
    Burnaby

    Oct 10, 2023: Tue, 2:30–4:20 p.m.
    Burnaby

    Oct 10, 2023: Tue, 2:30–4:20 p.m.
    Burnaby

    Sep 6 – Dec 5, 2023: Wed, 2:30–3:20 p.m.
    Burnaby

  • Exam Times + Location:

    Dec 9, 2023
    Sat, 12:00–3:00 p.m.
    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. We will discuss several standard application areas and also discuss some of my current research and novel approaches.

This is a computational science course that will help students develop their problem solving skills and help them make practical decisions when it comes to algorithm design in the context of a variety of problems in molecular biology and genomics. Bioinformatics is a huge industry and current hot research area. Bioinformaticians and Comutational Biologists work in a variety of settings including Cancer Agencies, Therapeutics, Pharmacology, Research Labs, Genomics Companies, and the Pharmaceutical Industry. 

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 final exam in order to pass the course.

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

REQUIRED READING NOTES:

Your personalized Course Material list, including digital and physical textbooks, are available through the SFU Bookstore website by simply entering your Computing ID at: shop.sfu.ca/course-materials/my-personalized-course-materials.

Registrar Notes:

ACADEMIC INTEGRITY: YOUR WORK, YOUR SUCCESS

SFU’s Academic Integrity website 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

RELIGIOUS ACCOMMODATION

Students with a faith background who may need accommodations during the semester are encouraged to assess their needs as soon as possible and review the Multifaith religious accommodations website. The page outlines ways they begin working toward an accommodation and ensure solutions can be reached in a timely fashion.