Bioinformatics and Computational Biology BCB420 H1 - Computational Systems Biology

Goals, Audience and Prerequisites

This course is an introduction to current concepts in computational systems biology - analysing the results of large scale, cross-sectional experiments on living cells, modelling the composition and connections of their constituent systems, and prediction of function and phenotypes. BCB 420 is one of the required courses in the Bioinformatics and Computational Biology Specialist Program, but the course is also open to interested 4th. year majors and specialists in life-science PoSts. The prerequisites include one advanced course in molecular biology or genetics and one introductory course in bioinformatics or genomics. Alternative preparation is possible and may be considered on a case-by-case basis. (Posted prerequisites will be waived by the coordinator accordingly).

Format

The course will be taught in the winter term of the 2007/2008 academic year. We will focus on one particular topic each week. In the first lecture we will introduce the topic and distribute reading assignments. The second lecture will be dedicated to presentation of key papers and in-depth discussion of interesting issues. The theoretical part of the course will be complemented by one project-based assignment. Topics will be determined jointly with the course-coordinator and developed in a collaborative, Wiki-based environment. For example students in the BCB Specialist Program may develop a Cytoscape plugin or equivalent piece of software, students who do not have programming skills might develop a workflow for data integration across various sources with the goal of functional annotation of a gene, or interpretation of a high-throughput experiment.

Grading

2 presentations worth 15% each One assignment worth 30% A final exam worth 30 % Active participation 10%

Enrolment

Enrolment will be capped at 15 students and priority will be given to students in the BCB program, for whom this is a required course. However interested students from other programs are explicitly encouraged to enrol. Contact the course coordinator.

Place and time

BCB420 is taught in the Winter session of the Academic Calendar (first lecture: January 7. 2008). It is scheduled for Monday and Wednesday at 10:00, in the Medical Sciences Building, MSB 3264.

Syllabus

Week Date Topic Instructor 1 Jan 7 Introduction, organisation, a one-lecture survival course in Bioinformatics (databases, services, tools and where to find information) Wodak / Steipe 2 Jan 14 Systems-biology data sources: genomics and proteomics and their associated databases Wodak 3 Jan 21 Computational tools and concepts: graph theory, graph types and metrics, cytoscape, R and informal programming Wodak 4 Jan 28 Gene regulatory networks Morris 5 Feb 4 Signal transduction networks N. N. 6 Feb 11 Metabolic networks Wodak   Feb 18 Reading Week - no classes   7 Feb 25 Data integration I: Combining datasets to improve annotation quality Vlassblom 8 March 3 Systems and module discovery: mutual information, clustering, network metrics Wodak 9 March 10 Computable models: representation (SBML, CellML), methods (PDEs, Petri Nets, Cellular Automata) and examples (E-Cell, M-Cell, Virtual Cell) Parkinson 10 March 17 Flux balance analysis Mahadevan 11 March 24 Synthetic biology Parkinson 12 March 31 Project week   13 April 7 Project week and project presentations

For further information

Brenda Bradshaw     Tel: 416-978-2700     Email: brenda.bradshaw@utoronto.ca University of Toronto Undergraduate Administration Department of Biochemistry 1 King's College Circle, Rm. 5207 Toronto, Ontario M5S 1A8 Fax: 416-978-8548 www.biochemistry.utoronto.ca Prof. Shoshana Wodak     Tel: 416-813-6351     Email: shoshana@sickkids.ca BCB420H1 Course Coordinator Hospital For Sick Children, Research Institute 180 Dundas Street, Suite 1300 Toronto, Ontario biochemistry.utoronto.ca/wodak/bch.html

Last update: December 21. 2008