THE UNIVERSITY OF BRITISH COLUMBIA
BIOF 501A (3) SPECIAL TOPICS IN BIOINFORMATICS
Instructor:
Ryan Brinkman
BC Cancer Research Centre
rbrinkman@bccrc.ca
Classes:
Winter Term 1
Thursdays 2:30 – 5:00 pm;
And 2nd Thursday of the month – attendance at Vancouver Bioinformatics User Group (VanBUG) 6:00 10:30 pm (this runs from September until April).
Course Objectives
This is a 3-credit discussion-based graduate course that acquaints the students with the latest developments
in bioinformatics analysis and algorithms. It runs in conjunction with the Vancouver Bioinformatics User
Group (VanBUG) Seminar Series (http://vanbug.org), in which the students will have an opportunity to
meet and discuss their work with both local and international guest speakers. During this course, students
will prepare presentations (individually and in groups) on recent papers in bioinformatics, genomics and
proteomics. Students will conduct a research literature survey and will present their results to the class to
stimulate discussion. In this self-directed learning assignment, students will work in teams and prepare 20
minute presentations. Participants are expected to conduct a library research project involving a review of
the literature on particular topics in the field of bioinformatics, proteomics, genomics and systems biology.
The review of the literature will include a summary of the most relevant articles published by researchers in
the particular fields mentioned, focusing on the areas that are currently considered as “hot topics” (focus
should be on papers published in the last 6 months). The literature review should demonstrate the student’s
ability to search information and to identify the critical articles that are most relevant to the topic of
interest. Students are also expected to identify areas of controversy, if possible, in the field where the
research results have opposing views.
Course Format
The course meets once a week, and runs in conjunction with the VanBUG Seminar Series.
Course Requirements
The course is mandatory requirement of the Bioinformatics Graduate Program; therefore admission to the
program ensures eligibility. Other students may join with permission of the lead instructor, space
permitting.
Enrollment Restrictions
Due to the format of the class, numbers will be limited to a maximum of 12, to allow adequate presentation
time to enrolled students.
Preparation
Students will be expected to have their presentations well-prepared, and if not presenting that day, they
should have prepared questions for their fellow students.
Grading
Based on two individual (33%) and two group presentations (33%) of different lengths, followed by 10
minutes of questions from students and instructors. Overall participation in class (reading assigned work
and asking questions in class (33%).
UBC Curriculum Proposal (v1/04)
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THE UNIVERSITY OF BRITISH COLUMBIA
Course Organization.
Classes are held every Thursday for 13 weeks:
Week 1 – Introductory class
Week 2 – VanBUG
Week 3 – 4 X 30 minute student presentations (A).
Week 4 – 4 X 30 minute student presentations (A).
Week 5 – 4 X 30 minute student presentations (A).
Week 6 – VanBUG
Week 7 – 6 X 20 min student presentations (B).
Week 8 – 6 X 20 min student presentations (B).
Week 9 - 3 X 30 min student presentations (C).
Week 10- VanBUG
Week 11 - 4 X 30 min student presentations (D).
Week 12 - 4 X 30 min student presentations (D).
Week 13- 4 X 30 min student presentations (D).
Group Composition: Student chose for group partners. Three groups of 4 students, with a balance of
computer science vs. biology-focused students.
Paper Selection: Papers will be chosen from a selection provided by the instructor. Paper selection should
be decided one week before the presentation and instructor should be informed of
selection by email. Presentation should be posted on web prior to presenting to the class.
Group A – 30 minutes: individual review of selected area of bioinformatics research.
Group B – 20 minutes: short dissection of “short” research paper-one aspect of paper can be a methodology
or important result. Try to place in a larger context of significance of results.
Group C – 30 minutes: presentation of groups and topics to class justifying the area of interest. Illustrate
and justify by a short description of the most important papers relevant to the area.
Group D – 30 minutes: presentation of groups of bioinformatics research area. In this exercise the paper
will be covered in more depth. It should be a challenging article published in a high-impact
journal such as Nature.
Required Texts: none
Recommended Text: A.D. Baxevanis and B.F.F. Ouellette (ed.), Bioinformatics: A practical guide to the
analysis of genes and proteins, 3rd edition. 2004. John Wiley & Sons, USA.
Prerequisites: None, but must have permission from instructor to register. Mandatory class for
Bioinformatics graduate program students, so space is limited.
UBC Curriculum Proposal (v1/04)
2