CISC/BCHM 875 Bioinformatics

Winter 2007

Instructor: Janice Glasgow

Office: Room 662 Goodwin Hall
Email: janice@cs.queensu.ca
Office Hours: Drop in or by email appointment

The course will be taught in collaboration with Parvin Mousavi (pmousavi@cs.queensu.ca).

Course Description

The emphasis of this course will be on current research topics that involve the application of computing concepts and techniques to problems in molecular biology. The course will consist of invited seminars (by Queen's professors and visitors from industry and other institutions) and student-led discussion of papers. Topics may include (but are not restricted to) DNA data analysis (genomics), machine learning applied to the analysis of microarray data, mathematical modeling and reverse engineering of biological systems, secondary and tertiary structure analysis and phylogenetics.

Evaluation will be based on class participation, paper and seminar reviews and a research term project:

• 10% for overall class participation, e.g., contribution to discussion of papers, attendance and participation in seminars given by outside speakers.
• 10% for seminar reviews. These are brief (1 page) overviews of the seminars for the course. At least 10 reviews must be completed to receive full marks.
• 10% for presentation (15-20 minutes) and leading class in discussion of current research paper.
• 10% for project proposal which is due Thursday February 15. Proposal should be a maximum of 5 pages and contain sections on: motivation and goals, background, and plan/methodology. It should demonstrate that you have completed your background reading for the project and have a clear plan for completing your work. Joint projects are encouraged, particularly among people from different disciplines.
• 10% for project presentation. These will be given during the last two Thursdays of the term. They should be approximately 15-20 minutes in length.
• 50% for final project report. These should be 15-20 pages in length. The report should include (but not be restricted to) the following sections : introduction, problem domain, computational techniques used, methodology, results and conclusions. Final projects are due Thursday April 30.

Meeting Times

• Tuesday 11:30 - 1:30 in Goodwin 521
• Thursday 12:30 - 1:30 in McLauglin 315

Thursday classes will consist of seminars and will be held jointly with CISC 471, Computational Biology. Tuesday classes will mostly consist of student presentations and research paper discussions.

Scheduled Speakers

January 9 Introduction to course

January 11 Don Forsdyke, Queen's Chargaff's Four Rules

January 16 Janice Glasgow, Queen's Case-based reasoning and molecular biology Case-based reasoning and molecular biology

January 18 Dr. Harriet Fellotter, Director Queen's Microarray Facility Microarrays in practice January 23

January 25 Dr. Parvin Mousavi Microarray analysis January 30

February 1 Brent Wathen Protein structure prediction February 6

February 8 Laurie Graham, Queen's Biochemistry Phylogenetic analysis February 13

February 15 Dr. Larry Greller, CSO and Director Biosystemix Mathematical approaches in bionformatics February 27

February 29 Parvin's midterm find room for class March 6

March 8 Janice Glasgow Protein structure determination March 13

March 15 2:30 Dr. Parvin Mousavi Sequence Similarity March 20

March 22 Dr. Roland Somogyi, Biosystemix Systems Biology

March 27 Hagit Shatkay, Queen's Computing Bioinformatics text mining

March 29 Dr. Paul Young, Queen's Substitution Matrices April 3

April 5 Steve Scribner, PARTEQ Intellectual Property

Those who would like an overview of certain topics in Bioinformatics should check out the schedule for CISC 471, which will have lectures on a number of topics in the area. Students with limited background in the life sciences are encouraged to read the overview paper Molecular biology for computer scientists.

Useful Web Sites

• International Society for Computational Biology (ISCB)
• Canadian Bioinformatics Web Site
• NIH web site
• UBC links directory
• Pubmed

 
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