BIOF 501 - Graduate Studies - University of British Columbia

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THE UNIVERSITY OF BRITISH COLUMBIA

UBC Curricul
um Proposal (v1/04)


1

UBC Curriculum Proposal Form

Change to Course or Program

Category: (1
)

Faculty:
Graduate Studies

Department:
Bioinformatics

Graduate
program

Faculty Approval Date:


Effective Session
:

Winter, Term
1


Year:

2007

for Change


Date:
September 20, 2006

Contact

Person:

Sharon Ruschkowski

Phone:
604
-
707
-
5803

Email:
sharonr@bcgsc.ca

Proposed Calendar Entry:


BIOF 501(3) SPECIAL TOPICS IN
BIOINFORMATICS








URL:



Present Calendar Entry:

N
/A


Type of Action:

New Course
.


Rationale:


Our new Bioinformatics graduate
program was approved by Senate in June 2006 and
we are registering our MSc and PhD students this
Sept 2006 in BIOF 599 or BIOF 699
,
respectively
.

This course has run since 2002 as

GENE501.
We were using GENE course numbers
for our bioinformatics courses, as they allowed t
his
while we were getting
our program
formally
established

at UBC.
It is appropriate now that this
course be given a formal BIOF number as part of
the new bioinfor
matics graduate program.


















BIOF 501

(3)
SPECIAL TOPICS
IN BIOINFORMATICS


Instructor:

Francis Ouellette

Director,
UBC
Bioinformatics Centre

604
-
822
-
3648

francis@bioinformatics.ubc.ca

THE UNIVERSITY OF BRITISH COLUMBIA

UBC Curricul
um Proposal (v1/04)


2


Class
es:

Winter Term 1

Thursdays 2:30



5:00 pm
;


A
nd 2
nd

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 c
ourse
that
acquaints the students with the latest developments
in bioinformatics analysis and algorithms
.
It runs in conjunction with the Vancou
ver Bioinformatics User
Group (V
an
BUG) Seminar Series

(http://vanbug.org)
, in which the students will have an op
portunity to
meet and discuss their work with both local and international guest speakers.

During this course
,

students
will prepare presentations (individually and
in
group
s
) on recent papers in bioinformatics, genomics and
proteomics. Students will cond
uct 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
min
ute

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 permissio
n 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 th
eir 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 quest
ions from students and instructors. Overall participation in class (reading assigned work
and asking questions in class (33%).







Course Organi
z
ation.

Classes are held every Thursday for 13 weeks:


Week 1


Introductory class


Week

2


VanBUG
-

Dr.
Ham
id Bolouri
from the
Institute for Systems Biology, Seattle, WA.

THE UNIVERSITY OF BRITISH COLUMBIA

UBC Curricul
um Proposal (v1/04)


3


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


Dr. Ron Beavis fro
m the Biomedical Research Centre, UBC.


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


Dr. Holger Hoos from the Computer Science department,
UBC


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
compu
ter 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. Prese
ntation 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 methodolo
gy
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 pape
rs 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.



Requir
ed Texts
: none


Recommended Text:

A.D. Baxevanis and B.F.F. Ouellette (ed.), Bioinformatics: A practical guide to the
analysis of genes and proteins, 3
rd

edition. 2004. John Wiley & Sons, USA.