Fall 2017 - CMPT 711 G100

Bioinformatics Algorithms (3)

Class Number: 7111

Delivery Method: In Person

Overview

Course Times + Location:

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

Instructor:
Leonid Chindelevitch
leonid@sfu.ca
1 778 782-4973

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:

Please note - this course is cross-listed with CMPT 441

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

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:

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

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