Difference between revisions of "Bioinformatics Main Page"
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| − | <small>''' | + | <small>'''These wiki pages are provided to coordinate information, activities and projects in the introductory bioinformatics course taught by Boris Steipe at the University of Toronto'''. If you are not one of my 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 [http://en.wikipedia.org/wiki/Bioinformatics Wikipedia article on bioinformatics], or visit [http://www.openwetware.org/wiki/Wikiomics Wikiomics]. Contact boris.steipe(at)utoronto.ca with any questions you may have.</small> |
== The Course == | == The Course == | ||
| − | + | BCH441H1F is the undergraduate course code and BCH1441H1F is the corresponding cross-listed course code for graduate students. | |
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===Organization=== | ===Organization=== | ||
;Dates | ;Dates | ||
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| + | The course will be next held in the Fall Term - September to December 2012. | ||
:Lectures: Monday, 13:00 to 14:00 and Thursday, 12:00 to 13:00 | :Lectures: Monday, 13:00 to 14:00 and Thursday, 12:00 to 13:00 | ||
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| + | <table cellpadding="5"> | ||
| + | |||
| + | <tr class="sh"> | ||
| + | <td><b>Activity</b></td> | ||
| + | <td><b>Weight</b><br><small>(Undergraduates)</small></td> | ||
| + | <td><b>Weight</b><br><small>(Graduates)</small></td> | ||
| + | </tr> | ||
| + | |||
| + | <tr class="sp"><td colspan="3" style="height: 5px;"></td></tr> | ||
| + | |||
| + | <tr class="s2"> | ||
| + | <td>[[Quizzes|'''9 In-class quizzes''']]</td> | ||
| + | |||
| + | <td>35 marks <small>(9 x 6)</small></td> | ||
| + | <td>25 marks <small>(9 x 5)</small></td> | ||
| + | </tr> | ||
| + | |||
| + | <tr class="s1"> | ||
| + | <td>[[Open project|'''Open project''']]</td> | ||
| + | <td>18 marks</td> | ||
| + | <td>18 marks</td> | ||
| + | </tr> | ||
| + | |||
| + | <tr class="s2"> | ||
| + | <td>[[Participation|'''"Classroom" participation''']]</td> | ||
| + | <td>8 marks</td> | ||
| + | <td>8 marks</td> | ||
| + | </tr> | ||
| + | |||
| + | <tr class="s1"> | ||
| + | <td>[[Graduate project|'''Graduate project''']]</td> | ||
| + | <td> </td> | ||
| + | <td>9 marks</td> | ||
| + | </tr> | ||
| + | |||
| + | <tr class="s2"> | ||
| + | <td>[[Exam questions|'''Final exam''']]</td> | ||
| + | <td>20 marks</td> | ||
| + | <td>20 marks</td> | ||
| + | </tr> | ||
| + | |||
| + | <tr class="sp"><td colspan="3" style="height: 5px;"></td></tr> | ||
| + | <tr class="s1"> | ||
| + | <td>'''Total'''</td> | ||
| + | <td>100 marks</td> | ||
| + | <td>100 marks</td> | ||
| + | </tr> | ||
| + | |||
| + | </table> | ||
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== Assignments == | == Assignments == | ||
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== Temporary links for material == | == Temporary links for material == | ||
| − | ===Lecture slides=== | + | ===Lecture slides 2012=== |
| + | |||
| + | ''None yet.'' | ||
| + | |||
| + | ===Lecture slides 2011=== | ||
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*[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/01-Introduction.pdf 01 - Introduction to the course <small>(pdf, 6.1 MB)</small>] | *[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/01-Introduction.pdf 01 - Introduction to the course <small>(pdf, 6.1 MB)</small>] | ||
*[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/02-SequenceData.pdf 02 - Sequence Data <small>(pdf, 4.6 MB)</small>] | *[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/02-SequenceData.pdf 02 - Sequence Data <small>(pdf, 4.6 MB)</small>] | ||
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* [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/20-PredictingProteinStructure_II.pdf 20 - Structure Prediction II: ''ab initio'' Prediction <small>(pdf, 10.0 MB)</small>] | * [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/20-PredictingProteinStructure_II.pdf 20 - Structure Prediction II: ''ab initio'' Prediction <small>(pdf, 10.0 MB)</small>] | ||
* [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/22-Outlook-ComputationalSystemsBiology.pdf 22 - Outlook: Computational Systems Biology <small>(pdf, 2.4 MB)</small>] | * [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/22-Outlook-ComputationalSystemsBiology.pdf 22 - Outlook: Computational Systems Biology <small>(pdf, 2.4 MB)</small>] | ||
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| − | + | A selection of [[Bioinformatics lecture recordings 2011|Lecture recordings of the 2011 course]] is available. | |
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| + | === Add this material ===* Quantitative evolution: signals of recent change and selective pressure | ||
Revision as of 20:52, 29 December 2011
BCH441 - Bioinformatics
Welcome to the BCH441 Course Wiki.
These wiki pages are provided to coordinate information, activities and projects in the introductory bioinformatics course taught by Boris Steipe at the University of Toronto. If you are not one of my 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
BCH441H1F is the undergraduate course code and BCH1441H1F is the corresponding cross-listed course code for graduate students.
Organization
- Dates
The course will be next held in the Fall Term - September to December 2012.
- Lectures: Monday, 13:00 to 14:00 and Thursday, 12:00 to 13:00
- Tutorial sessions: Mondays, 12:00 to 13:00 for in-class quizzes, quiz debriefings, exam preparation and other activities, as the need arises.
- Location
- MSB 2173 (Medical Sciences Building)
- General
See the Course Web page for general information.
We are recommending Understanding Bioinformatics, Zvelebil & Baum, Garland 2008 as a background textbook for the course. (buy used at AbeBooks)
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
| Activity | Weight (Undergraduates) |
Weight (Graduates) |
| 5 Assignments | 15 marks (5 x 3) | 10 marks (5 x 2) |
| 5 In-class quizzes | 35 marks (5 x 7) | 25 marks (5 x 5) |
| Open project | 7 marks | 5 marks |
| "Classroom" participation | 3 marks | 3 marks |
| Graduate project | 17 marks | |
| Final exam | 40 marks | 40 marks |
| Total | 100 marks | 100 marks |
| Activity | Weight (Undergraduates) |
Weight (Graduates) |
| 9 In-class quizzes | 35 marks (9 x 6) | 25 marks (9 x 5) |
| Open project | 18 marks | 18 marks |
| "Classroom" participation | 8 marks | 8 marks |
| Graduate project | 9 marks | |
| Final exam | 20 marks | 20 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. However I may adjust marks is if we phrase questions ambiguously on quizzes or if I decide that the final exam was too long.
Assignments
Assignment 5 has been posted.
Due Monday, Dec. 5.
Temporary links for material
Lecture slides 2012
None yet.
Lecture slides 2011
- 01 - Introduction to the course (pdf, 6.1 MB)
- 02 - Sequence Data (pdf, 4.6 MB)
- 03 - Structure Data (pdf, 13.6 MB)
- 04 - Sequence Analysis I (pdf, 8.6 MB)
- 05 - Sequence Analysis II (pdf, 3.1 MB)
- 06 - Interpreting Protein Structure (pdf, 6.6 MB)
- 07 - Structural Domains (pdf, 5.8 MB)
- 08 - Genome Sequencing (pdf, 1.4 MB)
- 09 - Genome Annotation (pdf, 4.2 MB)
- 10 - Homology I: Principles (pdf, 2.6 MB)
- 11 - Homology II: Optimal Sequence Alignment (pdf, 2.6 MB)
- 12 - Homology III: BLAST (pdf, 2.6 MB)
- 13 - Homology IV: Multiple Sequence Alignment (pdf, 4.3 MB)
- 14 - Predicting Protein Structure I: Homology Modeling (pdf, 2.3 MB)
- 15 - Phylogenetic Analysis I (pdf, 3.3 MB)
- 16 - Phylogenetic Analysis II (pdf, 1.0 MB)
- 17 - Comparative Genomics
- 18 - Computational Systems Biology
- 19 - Statistics and Exploratory Data Analysis (pdf, 3.4 MB)
- 20 - Structure Prediction II: ab initio Prediction (pdf, 10.0 MB)
- 22 - Outlook: Computational Systems Biology (pdf, 2.4 MB)
A selection of Lecture recordings of the 2011 course is available.
=== Add this material ===* Quantitative evolution: signals of recent change and selective pressure
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