S.03-104

c

G3vJ

004

j

O

SIMON FRASER UNIVERSITY

Senate Committee on University Priorities

?

Memorandum

TO:

Senate

?

FROM: "

John Waterhouse

Chair, SCUP

Vice President, Academic

RE:

Graduate Diploma in Bioinformatics

?

DATE:

?

October 14, 2003

Attached is a proposal from the Faculties of Science and Applied Sciences and the

Department of Molecular Biology and Biochemistry and the School of Computing

Science for a Graduate Diploma in Bioinformatics.

The Senate Committee on University Priorities reviewed the proposal at its October 8,

S ?

2003 meeting. With minor edits which have now been incorporated into the document,

the proposal was unanimously approved.

Once approved by Senate, the proposal is to be submitted to the Board of Governors.

MOTION:

"That Senate approves and recommends to the Board of Governors the

proposal for a Graduate Diploma in Bioinformatics as outlined in

S.03-104

including new courses MBB 505, 506, 1,

?

3, 659, 669, 679.

)3

end.

c: M. Plischke, Acting Dean, Faculty of Science

B. Lewis, Dean, Faculty of Applied Sciences

J. Driver, Dean, Graduate Studies

B. Brandhorst, Chair, Dept. of MBB

M. Smith, Dept. of MBB

A. Gupta, School of Computing Science

---

PROPOSAL ?

FOR

?

GRADUATE DIPLOMA

?

IN ?

BIOINFORMATICS

S

S

Prepared by:

Dr. Michael J. Smith, Professor and Chair, Dept. Mo!. Biol. & Biochem.

Dr. Arvind Gupta, Professor of Computing Science & Scientific Director of MITACS

Revised October 10, 2003

.

GRADUATE DIPLOMA IN BIOINFORMATICS

---

U

The Department of Molecular Biology and Biochemistry in the Faculty of Science and the School of

Computing Science in the Faculty of Applied Science jointly propose a Graduate Diploma in Bioinformatic

This program will serve the needs of the scientific and business communities as well as support studen

sponsored by the CIHR Bioinformatics in Health Science Training Grant in which SFU is a full partner with the

University of British Columbia and the BC Genome Sciences Centre.

Bioinformatics emerged as a necessary support discipline for the emerging international genomics and

proteomics initiatives that have resulted in almost overwhelming amounts of data. The full use of the genomics

and proteomics databases requires specific skill sets that combine both computational (computer) and life

sciences background. The immediate need for personnel trained in the area of bioinfonnatics is outlined in a

number of sources including the white paper "Bioinformatics Curriculum Recommendations for

Undergraduate, Graduate and Professional Programs"

prepared by the Canadian Genetic Diseases Network

and the NIH report of

who are not part of the CIHR program are strongly encouraged to choose their courses from those offered at

SFU.

REQUIRED COURSES: (4 LECTURE FOR 12 UNITS; 2 PRACTICUM FOR 12 UNITS)

Wi)

MBB

441/841

(3)

Bioinformatics

SFU

2) CWT 341/881

(3)

Computational Molecular Biology

SFU

3) MBB/CMPT

505

(3)

Prob. Based Learn. In Bioinform.

SFU, BCCA, CMMT

4) M1BB/CMPT

506

(3)

Critical Research Analysis

SFU, UBC

5)

At least two of

Number

Units

Title

Location

MBB/CMPT 601

(6)

Research Rotation 1

SFU, UBC, BCCA

MBB/CMIPT 602

(6)

Research Rotation 2

SFU, UBC, BCCA

MBB/CMPT 603

(6)

Research Rotation 3

SFU, UBC, BCCA

5)

ELECTIVES:

3 courses chosen from: (3 FOR 9 UNITS)

MBB

435/835' ?

(3)

Genomic Analysis

SFU

MEDG

505'

(3)

Genome Analysis

UBC

MBB

442/842 (3)

Proteomics

SF0

MBB

6592

(3)

Special Topics in Bioinformatics

SF0

MBB

669

(3)

Special Topics in Genomics

SF0

MBB

679

(3)

Special Topics in Proteomics

SF0

MBB 831

(3)

Molec. Evol. Euk. Genomes

SF0

MBB

832

(3)

Molec. Phylog. Evol.

SF0

CMPT

7405

(3)

Database Systems ?

.

SF0

CPSC 536A

(3)

Topics in Algorithms and

Complexity-Bioinfonn.

UBC

CPSC

504

(3)

Advanced Database Design

.

and Data Mining

UBC

CPSC 304

(3)

Database Management and Design

UBC

CMPT

3544

(3)

Database Systems I

SF0

MBB

33 i'

(3)

Molecular Biology

SRI

CMPT 770

(3)

Computer Graphics

SRI

CMPT 878

(3)

Scientific Visualization

SF0

STAT

547

Statistical Problems Arising in Genomics ?

UBC

STAT 890

(4)

Statistical Inference from human

SRI

genetic data

'Credit will be given for only one of MBB

435

or MEDG

505.

2

Special topics courses are given upon student demand and instructor availability

STAT 890 is a Special Topics course number; course content will vary by

offering.

See the appended list of courses.

4 CPSC 304, CMPT 354, and MBB 331 will not count toward Elective requirements; they will be recommended if the student is

deficient in either computational or life sciences background..

Credit will be given for only one of CMPT 740 and CPSC

504.

C

---

SEMESTER I

?

SEMESTER II

? SEMESTER III

CORE COURSES:

MBB

441

or 841

CMPT

341

or 881

MBB/CMPT

506

MBB/CMPT

505

ELECTIVES:

ELECTIVES:

ELECTIVES:

1

OR 2 COURSES

I OR

2 COURSES

1 OR 2 COURSES

PRACTIC1JM I

PRACTICTJM

H

.

0

---

APPENDIX A: COURSES:

4

CMPT 341 INTRODUCTION TO COMPUTATIONAL BIOLOGY:

This course introduces students to the

fornputing science principles underlying computational biology. The emphasis is on the design, analysis and

implementation of computational techniques. Possible topics include algorithms for sequence alignment,

database searching, gene finding, phylogeny, and structure analysis.

CMPT 354

I

DATABASE SYSTEMS:

Focus is modeling, querying and processing databases, focusing on

relational databases. The topics include conceptual database design, entity-relationship model, relational data

model, query languages and introduction to SQL, file and record organization, indexing techniques, query

processing and optimization.

CMPT 7701 COMPUTER GRAPHICS:

This course covers advanced topics and techniques in computer

graphics such as solid modeling, curves and surfaces, fractals, particle systems, advanced rendering techniques,

animation, and post-production techniques. Research topics in virtual reality, human figure animation, CAD,

scientific visualization, and other areas will also be discussed.

CMPT 8781 SCIENTIFIC VISUALIZATION:

This course presents advanced topics in the field of scientific

visualization. Topics may include: an introduction to visualization (importance, basic approaches and existing

tools), abstract visualization concepts, human perception, visualization methodology, 2D and 3D display and

interaction, advanced techniques (polygon reduction, volume rendering, multivariate representations, parallel

algorithms, etc.) and virtual reality.

CMPT 8811 SPECIAL TOPICS IN THEORETICAL COMPUTING SCIENCE:

This course can be

Wil

luded in the study program only when the topic is:

Computational Molecular Biology:

In this course we

l study algorithms for the acquisition and analysis of information from Diatonic Sequence similarity;

Sequence alignment and multiple sequence alignment; String alignment and algorithms for optimal alignment;

Proteins and folding; Physical Mapping; Phylogenies.

Approval will be sought to reconstitute this special

topics course as a formal course having a distinct course number

and title.

CPSC 304

I

DATABASE MANAGEMENT AND DESIGN:

Focus is relational databases, dealing with

relational database design, relational database languages, and concepts related to the transaction processing

layer (top layer) of a database management system (DBMS).

CPSC 504

I

ADVANCED DATABASE DESIGN AND DATA MINING:

Organizing information as

relations. Information retrieval through queries against relations. Storing relations as data. Efficient storage and

retrieval of data needed by queries. Reliability integrity and security considerations in database design.

INFO 5011 CONCEPTS IN COMPUTATION:

Introduction to fundamental software concepts and object-

oriented approaches. Introduce the elements of logic and discrete mathematics that allow reasoning about

computational structures and processes. Study of fundamental algorithms and data structures with emphasis on

the importance of data structure choice and implementation for obtaining the most efficient algorithm for

solving a given problem.

INFO 502

1

CONCEPTS IN MOLECULAR BIOLOGY:

This course will provide an introduction to

molecular biology. Course topics will include DNA structure and function, gene expression, transcriptional

control, protein structure and function, Mendelian genetic analysis, signaling pathways and recombinant DNA

echnology.

MBB 441/841 BIOINFORMATIC ANALYSIS:

This course introduces the history of bioinformatics, classic

---

algorithms used in the field, common methods of macromolecule analysis (i.e. within areas of sequence

alignment, structure analysis, phylogenetic analysis, etc.) and an introduction to bioinformatics-related

programming and database connectivity. [MBB 841]

This

INFO

course

504

I

introduces

TOPICS IN

algorithms

ALGORITHMS

and their application

AND COMPLEXITY

in bioinformatics

- BIOINFORMAflCS:

Topics include sequence

?

alignment,

•

phylogenetic tree reconstruction, prediction of RNA and protein structure, gene finding and sequence

annotation, gene expression, and biomolecular computing. A solid understanding of principles for design and

analysis of algorithms. Some assignments will involve use and extension of software tools, and others will

involve written studies of algorithms and their analysis. [CPSC

536A]

MBB/CMPT 505 PROBLEM BASED LEARNING IN BIOINFORMATICS:

The problem-based

learning course will develop students' ability to exchange ideas in small groups focused on real but simplified

problems in bioinfonnatics. Problems will be carefully selected to cover all aspects of bioinformatics research.

The core curriculum is identical during the first year for the graduate diploma and master's students.

MBB/CMPT 506 CRITICAL RESEARCH ANALYSIS:

This key seminar series aims to bring to the

students recognized Bioinformaticians from around the world. This will provide a forum for the students to

interact with these individuals and learn about their latest research. A class prior to each seminar would

augment the seminars where student presentations will help discuss in depth salient papers from the speakers

laboratory.

MBB/CMPT 601 BIOINFORMATICS RESEARCH ROTATION I:

One semester of original

bioinformatics research conducted in the lab of a designated mentor. Students are required to write their results

in a scientific journal format and defend these results before a panel consisting of the project mentor plus two

MBB/CMPT

other qualified

602

faculty

BIOINFORMATICS

members.

?

RESEARCH ROTATION II:

One semester of original

0

bioinformatics research conducted in the lab of a designated mentor. Students are required to write their results

in a scientific journal format and defend these results before a panel consisting of the project mentor plus two

other qualified faculty members.

MBB/CMPT 603 BIOINFORMATICS RESEARCH ROTATION III:

One semester of original

bioinformatics research conducted in the lab of a designated mentor. Students are required to write their results

in a scientific journal format and defend these results before a panel consisting of the project mentor plus two

other qualified faculty members.

MBB 842

1

PROTEOMICS:

Transition state theory; specificity in enzyme catalyzed reactions; use of

recombinant DNA techniques to describe and modify enzyme catalysis, the function of enzymes in organic

solvents, and the development of new catalytic activities through monoclonal antibody techniques.

MBB 831 MOLECULAR EVOLUTION OF EUKARYOTE GENOMES:

Examination of the dynamics

of change in eukaryotic nuclear, mitochondrial, and chioroplast genome structure and organization including

mechanisms of gene conversion, transposition, and duplication. Consideration of the origin and function of

intron, satellite, and repeated DNA sequences.

MBB 835 GENOMIC ANALYSIS:

Topics include: structure and function of the genome with emphasis on

genome mapping and sequencing projects, and computational methods for genomic sequence analysis

comprising: methods in genomic research, construction of physical genomic maps, ESTs - use and purpose;

Sequencing strategies: ordered vs. random; high throughput sequencing; Collection and assembly of data; Gene

finding (prediction of genes from DNA sequence; Annotation and release of data; Comparative Genomic

analysis; Comparative Genomic analysis; Functional genomics; Genome organization; Future directions.

---

MEDG 505

GENOME

ANALYSIS: Investigation of genetic information as it is organized within genomes,

genetic and physical map construction, sequencing technologies, gene identification, database accessing and

•nteration functional organization of genomes from contemporary, historic and evolutionary perspectives.

STAT 890:

(SFU)

SPECIAL TOPICS:

A)

STATISTICAL METHODS IN BIOINFORMATICS:

Topics include: Univariate and

multivariate probability distributions, and conditional probability and independence; methods

of statistical inference; stochastic processes: Poisson processes and Markov chains;

continuous-time Markov chains, hidden Markov models and random walks; computer

intensive approaches to statistical inference and applications to sequence alignment, gene

finding and phylogeny.

B)

STATISTICAL INFERENCE FROM HUMAN GENETIC DATA

Topics include: Maximum likelihood (ML) estimation of allele frequencies; testing

hypotheses and modeling variation with population samples; gene counting and the EM

algorithm; and linkage and recombination.

C)

STATISTICAL GENETICS IIA:

Monte Carlo methods in genetic data analysis.

D)

STATISTICAL GENETICS IIB:

Medical genetic studies.

E)

STATISTICAL GENETICS IIC:

Quantitative traits.

STAT 547B :

(UBC)

STATISTICAL PROBLEMS IN GENOMICS:

This course will cover quantitative

problems arising from current research. We focus on areas in which a statistical approach provides a powerful

tool for separating signal from noise. Students will learn to translate genomic research questions into well-

defined computational problems. Solutions and algorithms are found which are both theoretically sound and

practical to implement. Selected topics: gene expression analysis, analysis of tissue and protein arrays, sequence

lignment and comparison, Hidden Markov Models.

7

---

22)

J. Kronstad (BL, UBC): fungal biology,

infection-specific gene expression.

23)

M. Leroux (MBB, SFU): protein structure

function, proteomics

24)

D. Mager (Terry Fox Lab, BCCA)

retroelements and their impact on the genome

25)

M. Marra (Genome Sciences Centre, BCCA)

26)

B. McNeney (SAS, SFU): stats,

epidemiology, public health

27)

T. Moeller (CS, SFU): Visualization

28)

D. Moerman (Zoology, UBC): C. elegans

knockouts

29)

R. Ng (CS, UBC): database systems,

algorithms for analysis of SAGE

30)

F. Ouellette (Centre for Bioinformatics, UBC)

31)

M. Paetzel (MBB, SFU): structural biology

and molecular modeling

32)

F. Pio (Molecular Biology & Biochemistry,

SFU)

33)

A. Rose (Medical Genetics, UBC): genetics of

C. elegans.

34)

M. Rosin (Cancer Control Research, BCCA):

predictive genetic markers for cancer.

35)

C. Schwarz (SAS, SFU): generalized linear

models and dynamics of animal populations;

36)

J. Scott (MBB, SF13): phage display libraries

& mol modeling

37)

D. Sen (MBB, SFU): combinatorial molecular

biology, microarray and nano-technologies.

38)

M.J. Smith (MBB, SFU): phylogeny,

organellar genomics

39)

P. Unrau (MBB, SFU): combinatorial

molecular biology and combinatorial

mutagenesis.

40)

E. Verheyen (MBB, SFU): molecular genetics

of Drosophila.

41)

K. Wang (CS, SF13): data mining, databases.

42)

W. Wasserman (CMMT)

I

or

APPENDIX B: LIST OF ASSOCIATE FACULTY:

1)

D. Baillie (MBB, SFU): Bioinformatics

2)

C. Bajdik (Cancer Control Research, BCCA):

cancer susceptibility within families

3)

C.Beh (MBB, SFU): functional genomics of

yeast, microarrays.

4)

A. Beckenbach (Biological Sciences, SFU):

molecular evolution and phylogeny.

5)

B. Brandhorst (MBB, SFU): embryogenesis,

gene expression

6)

F. Brinkman (MBB, SFU): Bacterial genomics

and bioinformatics

7)

A. Brooks-Wilson (Genome Sequence Centre,

BCCA): Cancer genomics and genotyping

8)

C. Dean (SAS, SFU): mapping rates and point

processes.

9)

W. Davidson (MBB, SFU): molecular,

population, and evolutionary genetics

10)

M. Ester (CS, SFU): data mining, databases

11)

B. Finlay (BL, UBC): bacterial genetics

12)

J. Graham (SAS, SFU): population genetics.

13)

A. Gupta (CS, SFU): algorithms for

computational biology

14)

R. Hancock (Micro, UBC): bacterial

genomics

15)

N. Harden (MBB, SFU): functional genomics

of signal transduction in Drosophila

16)

N. Hawkins (MBB, SFU): mol genetics and

cell biology of flies and nematodes

17)

B. Honda

(MBB,

SFU): chromosome

structure and transcriptional regulation

18)

P. Hoodless (Terry Fox Lab, BCCA):

developmental genetics

19)

S. Jones (Genome Sciences Centre, BCCA):

Program Director, Bioinformatics.

20)

P. Keeling (Botany, UBC): Molecular

evolution.

21)

T. Kirkpatrick (CS, SFU): human computer

interaction, scientific visualization, computer

graphics;

KEY: BL = Biotechnology Laboratory

CMMT = Centre for Molecular Medicine & Therapeutics

CS = Computer Science

MBB = Molecular Biology and Biochemistry

SAS = Statistics and Actuarial Science

r

8

---

Appendix

C

Appendix to Proposal for Graduate Diploma in Bioinformatics

Administrative Structure

The program will be housed in the Faculty of Science. It will be adminis-

tered by a co-ordinating committee of 4 faculty members: two appointed by

the Department of Molecular Biology and Biochemistry and two appointed

by the School of Computing Science. This committee will serve as Graduate

Program Committee for the diploma. The Graduate Program Chair will be

a member of the committee elected by the members of the committee.

Tuition Fees

The diploma will be treated as a fee per semester program with semester

fees equal to those for an MSc student in the Faculty of Science.

Prepared by Richard Lockhart, Chair

Faculty of Science Graduate Studies Committee

20 May 2003

I14LQ

2Y)

ir

.

---

APPENDIX D

Calendar Entry

Graduate Diploma in Bioinformatics

The Department of Molecular Biology and Biochemistry and the School of Computing

Science co-operate in offering the graduate diploma in bloinformatics. The

administrative home is within the Faculty of Science. The program is administered by a

co-ordinating committee consisting of two faculty members each from the Department of

Molecular Biology and Biochemistry and the School of Computing Science. This

committee serves as Graduate Program Committee for the diploma and the Graduate

Program Chair is a member of this committee elected by its members.

This diploma program is designed to provide advanced education in the area of

bioinformatics for students with a bachelor's degree in molecular biology, cell biology,

biochemistry, computer science, mathematics, or related disciplines. Admission to the

program is highly competitive. In addition to serving the needs of the scientific and

business communities, this program supports students sponsored by the CIHR

Bioinformatics in Health Science Training Grant in which SFU is a full partner with the

University of British Columbia and the BC Genome Sciences Centre. Students in this

program who are not part of the CIHR program are strongly encouraged to choose their

courses from those offered at SFU.

The program requires 33 units, consisting of four core courses (12 units), three elective

courses (9 units) and a minimum two semesters of practicum rotations (12 units).

Students must obtain a B or better in each class or practicum. Students will have an

advisory committee consisting of a senior mentor and two other participating faculty

members drawn from the faculty of SFU, UBC, and the BC Genome Sciences Centre.

In consultation with mentors the student will be assigned practicums based on the

student's needs, area of interest, and background. The results of the practicum

semester must be written in journal form that will be the subject of an oral presentation.

The advisory committee will grade both the oral presentation and written report.

Students must complete:

MBB 441-3/841-3 Bioinformatics

?

SFU

CMPT 341-31881-3 Spec.Topics: Computational Molecular Biology SFU

MBB/CMPT 505-3 Problem Based Learning in Bioinformatics

?

SFU, BCCA, CMMT

MBB/CMPT 506-3 Critical Research Analysis

?

SFU, UBC

plus at least two of

MBB/CMPT 601-6 Research Rotation I

?

SFU, UBC, BCCA

MBB/CMPT 602-6 Research Rotation 2

?

SFU, UBC, BCCA

MBB/CMPT 603-6 Research Rotation 3

?

SFU, UBC, BCCA

.

1]

plus three chosen

MBB 4353/83531

MEDG 50531

MBB 442-3/842-3

MBB 65932

MBB 669-3

From

Genomic Analysis

Genome Analysis

Proteom ics

Special Topics in Bioinformatics

Special Topics in Genomics

SFU

UBC

SFU

SFU

SFU

11,

/0

---

MBB 679-3

MBB83I-3

MBB832-3

CMPT 740-3

CPSC 536A-3

CPSC 504-3

CPSC 304-3d

CMPT 35434

MBB 331-3d

CMPT 770-3

CMPT 878-3

STAT 547-3

STAT 890-4

Special Topics in Proteomics

SFU

Molecular Evolution of Eukaryote Genomes

SFU

Molecular Phylogeny and Evolution

SFU

Database Systems

SFU

Topics in Algorithms & Compi. Bioinform

UBC

Advanced Database Design & Data Mining

UBC

Database Management and Design

UBC

Database Systems I

SFU

Molecular Biology

SFU

Computer Graphics

SFU

Scientific Visualization

SFU

Statistical Problems Arising in Genomics

UBC

Statistical Inference from Human Genetic Data SFU

1

Credit will be given for only one of MBB 435 or MEDG 505

2

Special topics courses are given upon student demand and instructor availability

STAT 890 is a Special Topics course number; course content will vary by offering.

4

CPSC 304, CMPT 354, and MBB 331 will not count toward Elective requirements; they

will be recommended if the student is deficient in either computational or life sciences

background.

Credit will be given for only one of CMPT 740 and CPSC 504

.

Semester I

Semester II

Semester

Ill

Core Courses:

MBB

441

or 841

CMPT34Ior88I

MBB/CMPT 506

MBB/CMPT 505

Electives:

Electives:

Electives:

1

or 2 courses

I or 2 courses

I or 2 courses

Practicum I

Practicum II

---

Simon Fraser University

?

New Graduate Course Proposal Form

Department: Molecular Biology and Biochemistry

?

?

Course Number: MBB

5

(concurrent with CMPT

5

Course Title: Critical research analysis

Course Description for Calendar

(append a course outline):

Advanced seminar series for bioinformatics.

Credit Hours:6 Vector: 0-0-6

?

Prerequisites (if any): Enrolled in GD in Bioinformatics

Estimated Enrolment: 10 ?

When the course will first

be offered: 03-01

Frequency of course offering.

Ad hoc:

Upon agreement of faculty member

and individual student.

Justification:

This is an advanced seminar series for the. GD, MSc,

and PhD programs in Bioinformatics.

This course consists of a sequence of seminars by leading bioinformaticians from around the world.

This

will

provide a forum for the students to interact with these individuals and learn about their latest research. A class

prior to each seminar would augment the seminars where student presentations will help discuss in depth salient

papers from the speakers laboratory.

Resources:

Faculty member(s) who will normally teach

this course;

append information about their competency to teach

the course: SEE APPENDED LIST:

Number of additional faculty members required in order to offer this course: 0

Additional space required in order to offer

this course

(append details):

0

kdditional specialized equipment required in order to offer this course

(append details):

N.A.

Additional Library resources required

(append details):

annually: $ 0 ?

one-time: $ 0

Any other resource implications of offering this course

(append details):

N.A.

If additional resources are required to offer this course, the department proposing the course should be

prepared to provide information on the source(s) of those additional resources.

Approvals:

Departmental Graduate Program Committee:

?

(

Date:

IT)Qc

S 2 - CO

-

'L-

Faculty Graduate Studies Committee:

?

O

1a

?

Date: ?

66-3

/ ô

(-

Faculty:

/1 ?

Date:

?

A

5; /_Q -3

Following approval by the Faculty, this form and all relevant documentation should be forwarded to the Assistant Director -

?

Graduate Studies in the Office of the Registrar for consideration by the Senate Graduate Studies Committee, the Senate Committee on

?

Academic Planning

and

Senate.

newcourseform

?

Form revised August 1995

1^1

12

---

Simon Fraser University ?

New Graduate Course Proposal Form

Department: Molecular Biology and Biochemistry

?

?

Course Number: MBB

505

(concurrent with CMPT

505)

Course Title: Problem based learning in bioinformatics

Course Description for Calendar

(append a course outline):

The problem-based learning course will develop

students' ability to exchange ideas in small groups focused on real but simplified problems in bioinformatics.

Problems will be carefully selected to cover all aspects of bioinformatics research. The core curriculum is

identical during the first year for post-graduate diploma and for master's students.

Credit Hours:6 Vector: 0-0-6

?

Prerequisites (if any): Enrolled in GD in Bioinformatics

Estimated Enrolment: 10

?

When the course will first be offered: 03-01

Frequency of course offering.

Ad hoc:

Upon agreement of faculty member and individual student.

Justification:

This is a problem-based course for the. GD, MSc, and PhD programs in Bioinformatics. Each

week, a specialist will present students with a problem

in

some area of bioinformatics. Students will work in

small teams under the guidance of the mentor. This course is designed to give students hands-on experience

with a variety of topics and techniques in bioinformatics and to teach a team based approach to solving

problems.

Resources:

Faculty member(s) who will normally teach this course;

append information about their competency to teach

.

the course:

SEE APPENDED LIST:

Number of additional faculty members required in order to offer this course: 0

Additional space required in order to offer this course

(append details): 0 ?

-

Additional specialized equipment required in order to offer this course

(append details):

N.A.

Additional Library resources required

(append details):

annually: $ 0

?

one-time: $ 0

Any other resource implications of offering this course

(append details):

N.A.

If additional resources are required to offer this course, the department proposing the course should be

prepared to provide information on the source(s) of those additional resources.

Approvals: ?

( ?

. ?

t --

Departmental Graduate Program Committee:

J- -

?

&.-

kL_ ?

Date:

?

... 2 C C2

Faculty Graduate Studies Committee:

?

a

?

(J/

?

Date: ?.00:?

/0 /

U -

Faculty:

Following approval by the Faculty, this form and all relevant documentation should be forwarded to the Assistant Director -

?

Graduate Studies in the Office of the Registrar for consideration by the Senate Graduate Studies Committee, the Senate Committee on

?

Academic Planning and Senate.

newcourseform ?

Form revised August 1995

.

13

---

Simon Fraser University

New Graduate Course Proposal Form

(pit

Department: Molecular Biology and Biochemistry

?

Course Number: MBB øi

(concurrent with CWT eT)

Course Title: Research Rotation I

Course Description for Calendar

(append a course outline):

One semester of original bioinformatics research

conducted in the lab of a designated mentor. Students are required to write their results in a scientific journal

format and defend these results before a panel consisting of the project mentor plus two other qualified faculty

members.

Credit Hours:6 Vector: 0-0-6

?

Prerequisites (if any): Enrolled in GD in Bioinformatics

Estimated Enrolment: 10

?

When the course will first be offered: 03-02

Frequency of course offering.

Ad hoc:

Upon agreement of faculty member and individual student.

Justification:

This is the research practicum of the

?

graduate Diploma Program in Bioinformatics. Each

student in this program is required to complete at least two research practicum semesters. This practicum is

designed to give the student the opportunity to do original bioinformatics research, to write a report on his/her

work in scientific format, and to defend the work with oral presentation to a panel of experts. All of these skills

are necessary to be an effective practical Bioinformatician.

Resources:

Faculty member(s) who will normally teach this course;

append information -about their competency to teach

the course:

SEE APPENDED LIST:

Number of additional faculty members required in order to offer this course: 0

Additional space required in order to offer this course

(append details): 0

Additional specialized equipment required in order to offer this course

(append details):

N.A.

Additional Library resources required

(append details):

annually: $0

?

one-time: $ 0

Any other resource implications of offering this course

(append details):

N.A.

If additional resources are required to offer this course, the department proposing the course should be

prepared to provide information on the source(s) of those additional resources.

Approvals:

?

-

Departmental Graduate Program Committee:

?

2

3 ?

Date:

\) C,

c

Faculty Graduate Studies Committee:

?

i9?

4 ?

Date:

2001/

1

Faculty: ?

iI/,

?

Date: ?

6/z

?

3

Following approval by the Faculty, this form and all relevant documentation should be forwarded to the Assistant Director - ?

Graduate Studies in the Office of the Registrar for consideration by the Senate Graduate Studies Committee, the Senate Committee on

?

Academic

Planning

and Senate.

newcourseform

?

Form revised August 1995

"it

---

Simon Fraser University

New Graduate Course Proposal Form

.

Department: Molecular Biology and Biochemistry ?

Course Number:

MBB4O

(concurrent with CMPTQJ

Course Title: Research Rotation

II

Course Description for Calendar

(append a course outline):

One semester of original bioinformatics research

conducted in the lab of a designated mentor. Students are required to write their results in a scientific journal

format and defend these results before a panel consisting of the project mentor plus two other qualified faculty

members.

Credit Hours:6 Vector: 0-0-6 ?

Prerequisites (if any): Enrolled in PGD in Bioinformatics

Estimated Enrolment: 10 ?

When the course will first be offered: 03-02

Frequency of course offering.

Ad hoc:

Upon agreement of faculty member and individual student.

Justification:

This is the research practicum of the Post-graduate Diploma Program in Bioinformatics. Each

student in this program is required to complete at least two research practicum semesters. This practicum is

designed to give the student the opportunity to do original bioinformatics research, to write a report on his/her

work in scientific format, and to defend the work with oral presentation to a panel of experts. All of these skills

are necessary to be an effective practical Bioinformatician.

Resources:

Faculty member(s) who will

normally teach this course;

append information about their competency to teach

the course:

SEE APPENDED LIST:

Number of additional faculty members required in order to offer this course: 0

Additional space required in order to offer this course

(append details): 0

Additional specialized equipment required in order to offer this course

(append details): N.A.

Additional Library resources required

(append details):

annually: $ 0 ?

one-time: $ 0

Any other resource implications of offering this course

(append details): N.A.

If additional resources are required to offer this course, the department proposing the course should be

prepared to provide information on the source(s) of those additional resources.

Approvals:

Departmental

?

Graduate Program Committee:

ç ?

s-' -

-.

?

?

*

(

Date: .

C ?

2

Faculty Graduate Studies Committee: ?

CI?. 4

?

Date:

Faculty: ?

Date:

Following approval by the Faculty, this form and all relevant documentation should be forwarded to the Assistant Director -

?

Graduate Studies in the Office of the Registrar for consideration by the Senate Graduate Studies Committee, the Senate Committee on

?

Academic Planning and Senate.

newcourseform ?

Form revised August 1995

.

/6'

---

Simon Fraser University ?

p.

New Graduate Course Proposal Form

Department: Molecular Biology and Biochemistry

?

?

Course Number: MBB

(concurrent with CMPT 6

Course Title: Research Rotation III

Course Description for Calendar

(append a course outline):

One semester of original bioinformatics research

conducted in the lab of a designated mentor. Students are required to write their results in a scientific journal

format and defend these results before a panel consisting of the project mentor plus two other qualified faculty

members.

Credit Hours:6 Vector: 0-0-6 ?

Prerequisites (if any): Enrolled in POD in Bioinformatics

Estimated Enrolment: 10 ?

When the course will first be offered: 03-02

Frequency of course offering.

Ad hoc:

Upon agreement of faculty member and individual student.

Justification:

This

is the research practicum of the Post-graduate Diploma Program in Bioinformatics. Each

student in this program is required to complete at least two research practicum semesters. This practicum is

designed to give the student the opportunity to do original bioinformatics research, to write a report on his/her

work in scientific format, and to defend the work with oral presentation to a panel of experts. All of these skills

are necessary to be an effective practical Bioinformatician.

Resources:

Faculty member(s) who will normally teach this course;

append information about their competency to teach

the course:

SEE APPENDED LIST:

is

Additional space required in order to offer this course

(append details): 0

Additional specialized equipment required in order to offer this course

(append details):

N.A.

Additional Library resources required

(append details):

annually: $ 0 ?

one-time: $ 0

Any other resource implications of offering this course

(append details):

N.A.

If additional resources are required to offer this course, the department proposing the course should be

prepared to provide information on the source(s) of those additional resources.

Number of additional faculty members required in order to offer this course: 0

Approvals:

Departmental

?

Graduate Program Committee:

(

Faculty Graduate Studies Committee:

Faculty:

z ?

cL

?

Date:

c'c.

.5 2c 2

Date: ?

o(O/?r

F

57

Al

Date: ?

c/3

Following approval by the Faculty, this form and all relevant documentation should be forwarded to the Assistant Director -

?

Graduate Studies in the Office of the Registrar for consideration by the Senate Graduate Studies Committee, the Senate Committee on

?

Academic

Planning

and Senate.

newcourseform

?

Form revised August 1995

.

I(1

---

Simon Fraser University

?

New Graduate Course Proposal Form

Department: Molecular Biology and Biochemistry

?

Course Number: MBB

659-3

Course Title: Special Topics in Bioinformatics

Course Description for Calendar

(append a course outline):

Consideration of recent research literature on

contemporary topics in bioinformatics.

Credit Hours: 3

?

Vector:3-0-0 ?

Prerequisites (if any): MBB 441 or 841; or Comp. Sci. 341 or 881

Estimated Enrolment:

5-10

When the course will first be offered: After 03-3.

Frequency of course offering. Upon demand not to exceed once per academic year

Justification:

This will be a detailed consideration of contemporary advances in bioiriformatics. The course

will allow an in depth examination of specific research topics of immediate interest to the student(s).

Resources:

Faculty member(s) who will normally teach this course;

append information about their competency to teach

the course:

F. Brinkman

(MBB),

A. Gupta (Comp. Sci).

Number of additional faculty members required in order to offer this course: 0

Additional space required in order to offer this course

(append details): 0

Additional specialized equipment required in order to offer this course

(append details):

n.a.

Additional Library resources required

(append details):

annually: $ 0

?

one-time: $0

Any other resource implications of offering this course

(append details):

n.a.

If additional resources are required to offer this course, the department proposing the course should be

prepared to provide information on the source(s) of

those additional resources.

Departmental

Approvals: ?

Graduate Program Committee:

A

IL

?

-

?

Date:

S

Faculty Graduate Studies Committee: ?

7.

2

?

Date: COJ (Oo'(

Faculty: ?

I(

LI4

Date: ?

123/63

Following approval by the Faculty, this form and all relevant documentation should be forwarded to the Assistant Director -

?

Graduate Studies in the Office of the Registrarfor consideration by the Senate Graduate Studies Committee, the Senate Committee on

?

Academic Planning and Senate.

neweourseform

?

Form revised August 1995

iq

---

COURSE OUTLINE: The course will be a combination of

faculty

lectures, student seminars, and practical computational

exercises based on the contemporary methods and literature

of

bitoinformatics. Since this is a special topics course a

specific list of topics can not be supplied but will vary with each offering and advances in the field.

?

0

COMPETENCY OF FACULTY:

Dr. Fiona Brinkman is a faculty member in the Department of Molecular Biology and Biochemistry. Her

research and teaching expertise is in bioinformatics. She has established an international reputation in this field, is

a

MSFHR Scholar, has given numerous short courses for the Canadian Bioinformtics network, has designed and offered our

regular Bioinformatics courses (MBB 441 and 841), and is

a

principal in the CIHR Training Grant in Bioinformatics.

Dr. Arvind Gupta is a full professor in the School of Computing Science with research and teaching expertise in

computational biology (bioinformatics). He is also a principal in the CIHR Training Grant in Bioinformatics and has

designed and taught Comp. Sci. 881 (Computational Biology). Dr. Gupta is also co-author of the proposal for

a

"Postgraduate Diploma in Bioinformatics" at Simon Fraser University.

n

.

IT

---

Simon Fraser University

?

New Graduate Course Proposal Form

Department: Molecular Biology and Biochemistry

?

Course Number MBB669-3

Course Title: Special Topics in Genomics

Course Description for Calendar

(append a course outline):

Credit Hours: 3 ?

Vector: 3-0-0

?

Prerequisites (if any): MBB

435

or 835

Estimated Enrolment: 5-10 When the course will first be offered: After 03-3

Frequency of course offering. Upon demand not to exceed once per academic year.

Justification:

This will be a detailed consideration of contemporary advances in genomics. The course will

allow an in depth examination of specific research topics of immediate interest to the student(s).

Resources:

Faculty member(s) who will normally teach

this course;

append information about their competency to teach

the course:

Dr. David Baillie, Dr. Michael J. Smith

Number of additional faculty members required in order to offer this course: 0

Additional space required in order to offer this course

(append details): 0

Additional specialized equipment required in order to offer this course

(append details): 0

Additional Library resources required

(append details):

annually: $ 0 ?

one-time: $ 0

Any other resource implications of offering this course

(append details): 0

0

f additional resources are required to offer this course, the department proposing the course should be

prepared to provide information on the source(s)

of those additional resources.

?

- -

Approvals:

?

- ?

(

Departmental Graduate Program Committee:

?

L Date:

?

Cc

Faculty Graduate Studies Committee:

?

Date:

Faculty:

?

Ite: ?

c7z

543

Following approval by the Faculty, this form and all relevant documentation should be forwarded to the Assistant Director -

?

Graduate Studies in the Office of the Registrarfor consideration by the Senate Graduate Studies Committee, the Senate Committee on

?

Academic Planning

and Senate.

newcourseform

?

Form revised August 1995

.

.

Iq

---

M 0 61 G

LCj

COURSE OUTLINE: The course will be a combination of faculty lectures, student seminars, and practical computational

exercises based on the contemporary methods and literature of genomics. Since this is a special topics course a specific

list of topics cannot be supplied but will vary with each offering and advances in the field.

COMPETENCY OF FACULTY: ?

0

Dr. David Baillie is Professor of Molecular Biology and Biochemistry and a Canadian Research Chair in

Genomics. He is an acknowledged international leader in the field of genomics. He has developed both our

undergraduate and graduate courses in genomics (MBB

435

and

835).

Dr. Michael J. Smith is Professor and Chair of the Department of Molecular Biology and Biochemistry. He has

worked on both genomic and organellar DNA for over 30 years. He developed and teaches the MEB graduate course on

"Molecular Evolution and Phylogenetics".

S

S

---

Simon Fraser University

?

New Graduate Course Proposal Form

Department: Molecular Biology and Biochemistry

?

Course Number: MBB 679-3

Course Title: Special Topics in Proteomics

Course Description for Calendar

(append a course outline):

Consideration of recent research literature on

contemporary topics in bioinformatics.

Credit Hours: 3

?

Vector:3-0-0 ?

Prerequisites (if any): MBB 442 or 842

Estimated Enrolment: 5-10 When the course will first be offered: After 03-3.

Frequency of course offering. Upon demand not to exceed once per academic year

Justification:

This will beadetailed consideration of contemporary advances in proteomicss. The course will

allow an in depth examination of specific research topics of immediate interest to the student(s).

Resources:

Faculty member(s) who will normally teach

this course;

append

information about their competency to teach

the course:

Dr. F. Pio, Dr. M. Paetzel

Number of additional faculty members required in order to offer this course: 0

Additional space required in order to offer this course

(append details): 0

Additional specialized equipment required in order to offer this course

(append details):

n.a.

Additional Library resources required

(append details):

annually: $ 0 ?

one-time: $ 0

&ny other resource implications of offering this course

(append details):

n.a.

If additional resources are required to offer this course, the department proposing the course should be

prepared to provide information on the source(s) of those additional resources.

Approvals:

?

, ?

ç.

Departmental Graduate Program Committee: / _ -

ii

?

Date: ?

'c

5,

2cc

Faculty Graduate Studies Committee:

?

0

?

(EZ'

?

Date:

?

CX2J(O6 (Lr

Faculty: ?

/1' jø,4

?

Date: ?

4/2

57703

Following approval by the Faculty, this form and all relevant documentation should be forwarded to the Assistant Director -

?

Graduate Studies in the Office of the Registrar for consideration by the Senate Graduate Studies Committee, the Senate Committee on

?

Academic

Planning

and Senate.

newcourseform

?

Form revised August 1995

---

COURSE OUTLINE: The course will be a combination of faculty lectures, student seminars, and practical computational,

exercises based on the contemporary methods and literature of proteomics. Since this is a special topics course a speci

list of topics cannot be supplied but will vary with each offering and advances in the field.'

?

to

COMPETENCY OF FACULTY:

Dr. F. Pio is a faculty member in the Department of Molecular Biology and Biochemistry. Dr. Pio has expertise

in both X-ray crystallographic protein structure studies but also proteomics. He is AS! Fellow, obtained one of the first

NSERC Genomics grants (to develop proteomics algorithms to analyze data bases for functional groups), and has

designed and taught the proteomics courses in this Department (MBB 442 and 842).

Dr. Mark Paetzel is a new faculty member in Molecular Biology and Biochemistry. He is expert in the field of

protein structure and function and is MSFHR Scholar. Dr. Paetzel has also been successful in spearheading a successful

CFI proposal for a protein X-ray diffraction facility in MBB. Dr. Paetzel is expert in proteomics and computational

methods applicable to analyses of protein structure and function.

0

Da

---

S

.

.

W.A.C. Bennett Library?

Simon Fraser University?

Memorandum

To: Michael Smith. Dept of MBB ?

From:

Gwen Bird

Head, Collections Management

Subject:

Library Assessments for MBB

505-506 ?

gbirdsfu.ca

Cc: Leslie Rimmer, Liaison Librarian for MBB

?

Date: June 23, 2003

Here is the Library's assessment for the following MBB/CMPT courses:

MBB 505 Problem based learning in Bioinformatics

MBB 506 Critical research analysis

These courses will be offered beginning in 2003-01 on an ad hoc basis, by agreement of a supervising

faculty member and the individual students.

MBB

505

is a problem-based course in which a specialist will present students with a problem in

bioinfonnatics. Students will work in teams under the guidance of the mentor.

MBB

506

is an advanced seminar led by bioinformaticians from around the world. Students will learn

about recent research, including preparation discussing salient papers from the -speaker's laboratory.

The specific topics under discussion in both courses will depend on recent advances in the field.

Therefore, only a general assessment of the Library's collection in bioinformatics can be provided.

The Library is already actively collecting material in this subject area, including monographs and the

following journals:

Briefings in Bioinformatics

BMC Bioinformatics

Bioinformatics

Computational biology and chemistry

Computers in biology and medicine

IEEE Transactions on Information Technology in Biomedicine

Information Processing Letters

Journal of Computational Biology

Proteomics

RECOMB: Proceedings of the Annual International Conference on Computational Molecular Biology

The Library's holdings are adequate to support these courses.

Costs: THERE ARE NO COSTS ASSOCIATED WITH THESE COURSES.

If you have any questions regarding these assessments, please don't hesitate to contact me by phone

(3263) or by email, gbird(sfu.ca .

---

W.A.C. Bennett Library?

Simon Fraser University?

Memorandum

To: Michael Smith, Dept of MBB ?

From:

Gwen Bird

Head, Collections Management

Subject:

Library Assessments for MBB 601, 602

?

gbirdsfu.ca

& 603

Date:

June 23, 2003

Cc: Leslie Rimmer, Liaison Librarian for MBB

Here is the Library's assessment for the following Research Rotation courses in MBB:

MBB 601-6 Bioinformatics Research Rotation I

MBB 602-6 Bioinformatics Research Rotation II

MBB 603-6 Bioinformatics Research Rotation III

These courses will be offered beginning in 2003-02 on an ad hoc basis, by agreement of a supervising

faculty member and an individual student. This is the research practicum component of the post-

graduate diploma in Bioinformatics, jointly offered by MBB and Computing Science. Each student in

the program will be required to complete at least two research practicum semesters.

The coursework will consist of original bioinformatics research conducted by the student, and the

writing of a report in scientific format, and the defense of this work with an oral presentation before a

panel of experts.

As it is not possible to predict the specific topics of the student research, only a general assessment of

the Library's collection in bioinformatics can be provided. The Library is already actively collecting

material in this subject area, including monographs and the following journals:

Briefings in Bioinformatics

BMC Bioinformatics

Bioinformatics

Computational biology and chemistry

Computers in biology and medicine

IEEE Transactions on Information Technology in Biomedicine

Information Processing Letters

Journal of Computational Biology

Proleomics

RECOMB: Proceedings of the Annual International Conference on Computational Molecular Biology

The Library's holdings are adequate to support these courses.

Costs: THERE ARE NO COSTS ASSOCIATED WITH THESE COURSES.

If you have any questions regarding these assessments, please don't hesitate to contact me by phone

(3263)

or by email, gbirdsfti.ca.

'2c1:

---

W.A.C. Bennett Library

S

Simon Fraser University

Memorandum

To: Michael Smith, Dept of MBB

?

From:

Gwen Bird

Head, Collections Management

Subject:

Library Assessments for MBB

659, 669 ?

gbirdsfu.ca

& 679

Date: June 23, 2003

Cc: Leslie Rimnier, Liaison Librarian for MBB

Here is the Library's assessment for the following Special Topics courses in MBB:

MBB 659-3 Special Topics in Bioinformatics

MBB 669-3 Special Topics in Genomics

MBB 679-3 Special Topics in Proteomics

These proposed courses will be offered after 2003-3 with an expected enrollment of

5-10

students.

These courses are part of the post-graduate diploma in Bioinformatics, jointly offered by MBB and

Computing Science.

There are regular course offerings in the areas of Bioinformatics, Genomics and Proteomics that are

supported by current library resources.

?

--

As these are Special Topics courses it is

difficult

to do a course assessment when the content can and

will likely change over time, and no specific course outline has been provided. Although no extra

Library resources are required at this time, the Library reserves the right to reassess the collection when

one of the Selected Topics course offerings is offered as a course of its own.

Costs:

THERE ARE NO COSTS ASSOCIATED WITH THESE COURSES.

If you have any questions regarding these assessments, please don't hesitate to contact me by phone

(3263) or by email, gbird(sfu.ca.

9