Computational Systems Biology Main Page

Computational Systems Biology

Welcome to the Computational Systems Biology Course Wiki.

This is our main tool to coordinate information, activities and projects in University of Toronto's computational systems biology course BCB420. If you are not one of our students, you can still browse this site, however only users with a login account can edit or contribute or edit material. If you are here because you are interested in general aspects of bioinformatics or computational biology, you may want to review the Wikipedia article on bioinformatics, or visit Wikiomics. Contact boris.steipe(at)utoronto.ca with any questions you may have.

The Course

Organization

Dates

Lectures: Monday, 10:00 to 11:00 and Wednesday, 10:00 to 11:00 (... according to the Calendar. However we will decide on more suitable times at the first meeting and most likely we will meet in one two-hour slot rather than in two slots.)

First lecture: Monday, January 9. 2012 at 10:00 - Organization.
Don't miss this lecture or you will immediately fall behind.

Location

MS 3290 (Medical Sciences Building) (In case there are changes they will be announced here.)

General

See the Course Web page for general information.

Textbook

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Submissions

This is an electronic submission only course; but if you must print material, you might consider printing double-sided. Learn how, at the Print-Double-Sided Student Initiative.

Grading and Activities

I have prepared a number of exercises for the course that I expect everyone to complete, however there will be no required submissions for these. Exercise-related questions as well as pre-reading related questions will be part of the weekly quizzes. Don't expect to do well on the quizzes unless you have done the exercises and completed the pre-reading carefully. This course demands a lot of your discipline and time-management. A large portion of your grade will be contributed by the Open Project. JTB2020 students will also complete a number of Applied Bioinformatics Exercises. Deliverables for the course will be completed well before end-of-term crunch time and there will be no final exam.

Activity	Weight BCB410 - (Undergraduates)	Weight JTB2020 - (Graduates)
9 In-class quizzes	54 marks (9 x 6)	36 marks (9 x 4)
Open project	30 marks	30 marks
"Classroom" participation	16 marks	16 marks
Applied Bioinformatics Exercises		18 marks
Total	100 marks	100 marks

A note on marking

It is not my policy to adjust marks towards a target mean and variance (i.e. there will be no "belling" of grades). I feel strongly that such "normalization" detracts from a collaborative and mutually supportive learning environment. If your classmate gets a great mark because you helped him with a difficult concept, this should never have the effect that it brings down your mark through class average adjustments. Collaborate as much as possible, it is a great way to learn. I may however adjust marks is if we phrase questions ambiguously on quizzes or if I decide that the final exam was too long.

Prerequisites

You must have taken an introductory bioinformatics course as a prerequisite, or otherwise acquired the necessary knowledge. Therefore I expect familiarity with the material of my BCH441. If you have not taken BCH441, please check the requirements below and update your knowledge and skills before the course starts. I will not make accommodations for lack of prerequisites. Please check the syllabus for this course below to find whether you need to catch up on additional material, and peruse this site to find the information you may need.

• Solid knowledge of the properties of the proteinogenic amino acids, their names and one-letter code;
• Understanding of the nature of sequence and structural data and the common formats in which such data is stored;
• Familiarity with the molecular visualization program VMD;
• Ability to view molecular structures in (wall-eyed) stereo;
• Familiarity with NCBI, EBI and PDB databases and services;
• Use of the EMBOSS suite of sequence analysis tools;
• Familiarity with the computation of multiple sequence alignments and the Jalview alignment editor;
• Computation and analysis of phylogenetic trees;
• Concepts of protein structure prediction; homology modeling;
• An introduction to statistics with R.

Exercises and Pre-reading

All course units will have associated exercises that are topics for the following week's quiz.

All course units will have assigned pre-readings that are topics for the current week's quiz.

Timetable and syllabus

 

I n t r o d u c t i o n
Week	Date	Lecturer	Contents	Activities
1	Jan. 9 - 14	Steipe	Introduction to Computational Systems Biology Course Organisation	—
D a t a
Week	Date	Lecturer	Contents	Activities
2	Jan. 16 - 21	Steipe	Databases and services GO, OMIM and other phenotype databases Data mining Data integration: Loose coupling, combining datasets to improve annotation quality, evidence combination Prediction of function	Quiz 1
"-omics"
Week	Date	Lecturer	Contents	Activities
3	Jan. 23 - 28	Steipe	Working with -ome scale data R and Bioconductor Clustering and partitioning Enrichment analysis informal programming with perl/php/MySQL/ IDE - Komodo, KDevelop (also Eclipse, except no Perl)	Quiz 2, project concept due
4	Jan. 30 - Feb. 3	Steipe	genomics transcriptome	Quiz 3
5	Feb. 6 - 10	Steipe	proteome, interactome metabolome, glycome, lipidome	Quiz 4, project outline due
I n t e r a c t i o n s ,   P a t h w a y s   a n d   N e t w o r k s
Week	Date	Lecturer	Contents	Activities
6	Feb. 13 - 17	Steipe	Cytoscape Graph theory, graph types and metrics; small-world or random-geometric, date-hubs and party-hubs	Quiz 5
	Feb. 20 - 24	Reading Week - School closed
7	Feb. 27 - Mar. 2	Steipe	The biology of protein-protein interactions; physical vs. genetic interactions Interaction databases Interaction prediction, Interologs	Quiz 6
S y s t e m s
Week	Date	Lecturer	Contents	Activities
8	Mar. 5 - 9	Steipe	Gene regulatory networks Signal transduction networks Metabolic networks KEGG, BioCYC	Quiz 7
9	Mar. 12 - 16	Steipe	Extracting regulatory networks from gene expression data Extracting systems from -omics datasets through mutual information	Quiz 8
10	Mar. 19 - 23	Steipe	Structural network analysis http://www.csb.ethz.ch/research/structural Systems dynamics http://www.csb.ethz.ch/research/dynamic	Quiz 9, project final submission due
M o d e l s
Week	Date	Lecturer	Contents	Activities
11	Mar. 26 - 30	Steipe	methods (ODEs, PDEs and their stochastic counterparts, Petri Nets, Cellular Automata) methods process calculi (pi-calculus, ) representation (SBML, CellML) examples (E-Cell, M-Cell, Virtual Cell)	—
12	Apr. 2 - 6	Steipe	constraint based modelling, Flux balance analysis Computational Synthetic Biology http://www.csb.ethz.ch/research/synthetic	—

In depth...

• Glossary
• Mutation Data Matrices
• Amino acids
• Database Identifiers

Resources

Course related

• The Course Google Group.
• Netiquette for the Group mailing list

Contents related

• The VMD tutorial
• A Stereo Vision tutorial
• MetaDatabase
• NAR January-2008 Database issue
• NAR July-2008 Web server issue

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