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.
Contents
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. Whatever you do, 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
- ???
- 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 |
|
— |
| F u n c t i o n a l A n n o t a t i o n | ||||
| Week | Date | Lecturer | Contents | Activities |
| 2 | Jan. 16 - 21 | Steipe |
|
Quiz 1 |
| "-omics" | ||||
| Week | Date | Lecturer | Contents | Activities |
| 3 | Jan. 23 - 28 | Steipe |
|
Quiz 2, project concept due |
| 4 | Jan. 30 - Feb. 3 | Steipe |
|
Quiz 3 |
| 5 | Feb. 6 - 10 | Steipe |
|
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 |
|
Quiz 5 |
| Feb. 20 - 24 | Reading Week - School closed | |||
| 7 | Feb. 27 - Mar. 2 | Steipe |
|
Quiz 6 |
| S y s t e m s | ||||
| Week | Date | Lecturer | Contents | Activities |
| 8 | Mar. 5 - 9 | Steipe |
|
Quiz 7 |
| 9 | Mar. 12 - 16 | Steipe |
|
Quiz 8 |
| 10 | Mar. 19 - 23 | Steipe |
|
Quiz 9, project final submission due |
| M o d e l s | ||||
| Week | Date | Lecturer | Contents | Activities |
| 11 | Mar. 26 - 30 | Steipe |
|
— |
| 12 | Apr. 2 - 6 | Steipe |
|
— |
In depth...
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
| 325C78 | 7097B8 | 9BACCF | A8A5CC | D7C0F0 |
