CS-3220/BIO-3220 - Introduction to Bioinformatics (Fall 2019)

Course Objectives

This course is an introduction to bioinformatics and a practical guide to the analysis of genes and proteins. It will familiarize students with the tools and principles of contemporary bioinformatics. By the end of the course, students will have a working knowledge of a variety of publicly available data and computational tools important in bioinformatics, and a grasp of the underlying principles that is adequate for them to evaluate and use novel techniques as they arise in the future. 

Course Information

• Instructor: Dr. Yingwei Wang 

• Email: ywang@upei.ca
• Web Page: www.csit.upei.ca/~ywang
• Office: CASS 407
• Lecture Time/Location: M W F 12:30-1:20, CSH104
• Office Hour: M W F, 10:30 - 12:20

• Lab Sessions: For this offering only: Because this course is scheduled in a computer lab, we will accomplish our lab work in class from time to time. Thus, we do not have separate lab sessions. The lab session time is only used when we need extra hours of teaching due to storm closures or other reasons.
• Prerequisite: CS2610 or BIO2230 or permission of instructor.
• Explanations to the prerequisite:
• This is an inter-discipline course. Ideally, students registered in this course should have computer science background and biological background. Because this prerequisite is hard to fulfill, in this course the prerequisite is set to that the background in only one area is required. The instructor will help students to obtain necessary knowledge that their background does not cover. For students from the Department of Computer Science, CS2610 (Data Structures and Algorithms) is required. For students from the Department of Biology, BIO2230 (Introductory Genetics) is required.
• For registrants not from the above two departments, the following possible reasons may lead them to register in this course: they may have practical experience related to bioinformatics; they may need bioinformatics knowledge in their work or research; they may be interested in bioinformatics very much. For these registrants, no specific prerequisite is required. A brief discussion with the instructor is enough. 
• Textbook:  Michael Agostino, Practical Bioinformatics, Garland Science, ISBN-13: 978-0815344568, ISBN-10: 0815344562
• All students, whether you are registered in CS3220, BIO3220, HUB8850, or VPM8850, use course CS3220 Moodle site. If you are registered in VPM8850 or HUB8850, please also check http:/vpm8850.cloudbasis.com. 

Evaluation

• Assignments 30%
• Midterm 25%
• Final exam 35% 
• Participation 10% (1% deduction for each absence. Maximal deduction is 10%. For compassionate reasons, no deduction for two absence. For health reasons, no deduction if a dated doctor's note is presented before or after; 0.5% deduction if no doctor's note but sent email to the instructor before class. No exception for other situations).
• For whatever reasons, if 50% or more of the classes were missing, the mark of the course will be 0. 

Major Topics

• Biological Databases
• Pairwise Sequence Alignments
• Multiple Sequence Alignments
• Phylogenetic Analysis
• Gene Prediction
• Mass Spectrometry
• Microarray