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Note that the information presented here does not necessarily reflect the most up to date syllabus or course information. Rather this information is intended to provide a general overview of course content from previous offerings.
Welcome to Computer Science 830, "Bioinformatics and Computational Biology". The prerequisites for CMPT 830 are a previous bioinformatics course or at least 6 credit units of previous course work in each of Computer Science, Statistics, and the life sciences.
This course provides an in-depth algorithms-based introduction to major concepts and techniques in bioinformatics. Expect to have to write real code, determine the complexity of an algorithm, or derive parameters for a probability distribution.
Ian McQuillan, Computer Science
email: mcquillan@cs.usask.ca
office: Thorv S423 (in the Spinks Addition)
telephone: 966-2900
Time: The time for the class is Tuesdays, Thursdays from 10:00 until 11:20 a.m.
Room: Arts 105
First Meeting: Thursday January 6, 2011
The following topics indicate the tentative areas to be covered:
Introduction to bioinformatics, Algorithms, Perl, Sequence alignment, Phylogenetic trees, Protein structure, RNA secondary structure, Microarrays, Mass spectrometry, Hidden Markov models, L systems, Information theory in natural computing.
There will be 2 or 3 assignments, to be completed on an individual basis.
There will be a final (take-home) exam whose date has yet to be scheduled.
There will be a project to be done individually. The topic must be relevant to bioinformatics, chosen by the student and approved by the instructor. The project will consist of both an oral presentation and a written survey paper.
assigments 25%
final exam 35%
project 40%
There will be no required textbook for the class. Certain books which are good suggested reading would be:
An Introduction to Bioinformatics Algorithms by Jones & Pevzner, 2004, published by MIT Press. Call No. QH324.2.J66 2004.
Introduction to Computational Molecular Biology by Setubal and Meidanis, PWS Publishing, 1997. Call No. QH506 .S4893 1997.
Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology by Gusfield, Cambridge University Press, 1997. Call No. QA76.9 .A43G87.
Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins by Baxevanis and Ouellette, Wiley-Interscience, 2005. Call No. QP620.B575 2005.
For those students who are looking for an introductory book on bioinformatics, an excellent book is Fundamental Concepts of Bioinformatics by D. E. Krane and M. L. Rayner, 2003, Benjamin Cummings. This book is also on Reserve, with Call No. QH324.2 .K72 2003.
Department Policy on Academic Honesty Students are expected to be academically honest in all of their scholarly work, including course assignments and examinations. Academic honesty is defined and described in the Department of Computer Science Statement on Academic Honesty and the University of Saskatchewan Academic Honesty Website.
