Difference between revisions of "Bioinformatics Main Page"
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This course will be taught again in September 2015. | This course will be taught again in September 2015. | ||
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| + | There will be extensive changes to integrate ''systems biology'' material into the syllabus. This will affect lecture topics, assignments and the marking scheme. Proceed with caution until this note has been removed. Contact the course coordinator with any questions you may have. | ||
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== The Course == | == The Course == | ||
| − | This course is an introduction to bioinformatics, for life science undergraduates and graduates and the specialists in the BCB Program. The course focusses on foundational techniques, the use of web sites for analysis, judicious interpretation of results and above all, proper, evidence based reasoning about biology. The | + | This course is an introduction to bioinformatics, for life science undergraduates and graduates and the specialists in the BCB Program. The course focusses on foundational techniques, the use of web sites for analysis, judicious interpretation of results and above all, proper, evidence based reasoning about biology. The course covers the analysis of single biomolecule sequence and structure, ''omics''-scale datasets, and the integration of biological data towards systems biology. The course is complemented by [[Computational_Systems_Biology_Main_Page|'''BCB420''']] (offered in the Winter Term) which consolidates aspects of cutting-edge computational systems biology in a project context. |
BCH441H1F is the undergraduate course code.<br> | BCH441H1F is the undergraduate course code.<br> | ||
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;General | ;General | ||
| − | :BCH441H is a bioinformatics survey course, cross-listed for graduate students as BCH1441H. The course provides an overview of current applications of computational techniques in life-science laboratories. It discusses the most important strategies and resources for annotation of biological sequences on the Internet, their judicious application, and the interpretation of results. Assignments will complement the lectures by practicing techniques of computational molecular data analysis, with an emphasis on Web based tools. Students will be introduced to the programming language and statistical workbench '''R''' | + | :BCH441H is a bioinformatics survey course, cross-listed for graduate students as BCH1441H. The course provides an overview of current applications of computational techniques in life-science laboratories. It discusses the most important strategies and resources for annotation of biological sequences on the Internet, their judicious application, and the interpretation of results. Assignments will complement the lectures by practicing techniques of computational molecular data analysis, with an emphasis on Web based tools. Students will be introduced to the programming language and statistical workbench '''R'''. |
;Dates | ;Dates | ||
:BCH441/BCH1441 is a Fall Term course. | :BCH441/BCH1441 is a Fall Term course. | ||
| − | : | + | :Tutorial sessions: Tuesday, 17:00 to 18:00 for open discussion of lecture material, in-class quizzes, quiz debriefings, exam preparation and other activities. Class begins at 10 minutes past the hour. |
| − | + | :Lectures: right after the tutorials: Tuesday, 18:00 to 20:00. | |
| − | + | ||
;Location | ;Location | ||
| − | :[http://map.utoronto.ca/utsg/building/005 MS | + | :[http://map.utoronto.ca/utsg/building/005 MS 4279] (Medical Sciences Building) |
| − | ;The [http://steipe.biochemistry.utoronto.ca/abc/students/ Student Wiki]. | + | ;The [http://steipe.biochemistry.utoronto.ca/abc/students/ '''Student Wiki''']. |
| − | :Many of your activities will take place on a [http://steipe.biochemistry.utoronto.ca/abc/students/ Wiki site] | + | :Many of your activities will take place on a [http://steipe.biochemistry.utoronto.ca/abc/students/ Wiki site (the "Student Wiki")]. |
| − | ;The [http://groups.google.com/group/ | + | ;The [http://groups.google.com/group/bch441_2015 Mailing List]. |
:All course announcements and all course discussion (outside of class) will take place on a mailing list. We use Google Groups for this purpose. You will be subscribed to the list in the first class. You will not be able to participate fully in the course if you are not subscribed. Make sure you are subscribed '''with the email address you use most frequently''' and set your preferences to immediate delivery - "Digest" or "Web only" delivery won't allow you to participate actively in discussions and your participation mark will suffer. | :All course announcements and all course discussion (outside of class) will take place on a mailing list. We use Google Groups for this purpose. You will be subscribed to the list in the first class. You will not be able to participate fully in the course if you are not subscribed. Make sure you are subscribed '''with the email address you use most frequently''' and set your preferences to immediate delivery - "Digest" or "Web only" delivery won't allow you to participate actively in discussions and your participation mark will suffer. | ||
| Line 62: | Line 65: | ||
;Office hours | ;Office hours | ||
| − | :I do not hold regular office hours. I prefer communication via e-mail | + | :I do not hold regular office hours. I prefer communication via e-mail since it leaves you with a document trail of what was discussed, and we can share points of general interest more easily with the class. If you feel you must have a face-to-face meeting, coordinate with me. |
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<div class="alert"> | <div class="alert"> | ||
| − | Syllabus and assignments may still undergo | + | Syllabus and assignments may still undergo changes throughout the term. |
</div> | </div> | ||
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;A note on marking | ;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. <small>However I may adjust marks is if we phrase questions ambiguously on quizzes or if I decide that the final exam was too long.</small> | + | 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. <small>However I may adjust marks is if we phrase questions ambiguously on quizzes, or if I decide that the final exam was too long.</small> |
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| − | <small>The lecture recordings linked below are copyrighted material, for the personal use of participants of the course only. It is not permissible to repost them elsewhere. If in doubt, ask me.</small> | + | <!-- small>The lecture recordings linked below are copyrighted material, for the personal use of participants of the course only. It is not permissible to repost them elsewhere. If in doubt, ask me.</small --> |
===I n t r o d u c t i o n=== | ===I n t r o d u c t i o n=== | ||
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<div class="table-intro-text">Bioinformatics focusses on the data and methods, and Computational Biology defines the objectives, to bring our understanding of Biology to a rigorous, principled, quantitative and predictive level. Over the last two decades, ever since bioinformatics began to take centre stage in the life sciences, the rate of change in the discipline has continuously accelerated. In part, driven by the growth of the Internet, in part through novel algorithms, but to the largest part driven through a very large increase in the volume and quality of data, opportunities for computational analysis in the life science lab have grown in leaps and bounds. One of the associated challenges is to keep abreast of the rapidly changing methods and tools that are available. This course focuses on the basic principles and concepts of the field and emphasis techniques and skills that are easily accessible and freely available to every life science researcher.</div> | <div class="table-intro-text">Bioinformatics focusses on the data and methods, and Computational Biology defines the objectives, to bring our understanding of Biology to a rigorous, principled, quantitative and predictive level. Over the last two decades, ever since bioinformatics began to take centre stage in the life sciences, the rate of change in the discipline has continuously accelerated. In part, driven by the growth of the Internet, in part through novel algorithms, but to the largest part driven through a very large increase in the volume and quality of data, opportunities for computational analysis in the life science lab have grown in leaps and bounds. One of the associated challenges is to keep abreast of the rapidly changing methods and tools that are available. This course focuses on the basic principles and concepts of the field and emphasis techniques and skills that are easily accessible and freely available to every life science researcher.</div> | ||
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* Course Organisation | * Course Organisation | ||
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| − | <!-- use template {{PDFlinkOld... after semester closes down --> | + | <!-- use template {{PDFlink... , then {{PDFlinkOld... after semester closes down --> |
| − | + | {{PDFlinkOld|[http://steipe.biochemistry.utoronto.ca/abc/CourseMaterials/BCH441/01-Introduction_2014.pdf Lecture notes 2014: 01 - Introduction <small>(PDF 5.9 MB)</small>]}}<br /> | |
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</td> | </td> | ||
Revision as of 16:55, 8 July 2015
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.
This course will be taught again in September 2015.
There will be extensive changes to integrate systems biology material into the syllabus. This will affect lecture topics, assignments and the marking scheme. Proceed with caution until this note has been removed. Contact the course coordinator with any questions you may have.
</div-->
Contents
The Course
This course is an introduction to bioinformatics, for life science undergraduates and graduates and the specialists in the BCB Program. The course focusses on foundational techniques, the use of web sites for analysis, judicious interpretation of results and above all, proper, evidence based reasoning about biology. The course covers the analysis of single biomolecule sequence and structure, omics-scale datasets, and the integration of biological data towards systems biology. The course is complemented by BCB420 (offered in the Winter Term) which consolidates aspects of cutting-edge computational systems biology in a project context.
BCH441H1F is the undergraduate course code.
BCH1441H1F is the cross-listed course code for graduate students.
Organization
- General
- BCH441H is a bioinformatics survey course, cross-listed for graduate students as BCH1441H. The course provides an overview of current applications of computational techniques in life-science laboratories. It discusses the most important strategies and resources for annotation of biological sequences on the Internet, their judicious application, and the interpretation of results. Assignments will complement the lectures by practicing techniques of computational molecular data analysis, with an emphasis on Web based tools. Students will be introduced to the programming language and statistical workbench R.
- Dates
- BCH441/BCH1441 is a Fall Term course.
- Tutorial sessions: Tuesday, 17:00 to 18:00 for open discussion of lecture material, in-class quizzes, quiz debriefings, exam preparation and other activities. Class begins at 10 minutes past the hour.
- Lectures: right after the tutorials: Tuesday, 18:00 to 20:00.
- Location
- MS 4279 (Medical Sciences Building)
- The Student Wiki.
- Many of your activities will take place on a Wiki site (the "Student Wiki").
- The Mailing List.
- All course announcements and all course discussion (outside of class) will take place on a mailing list. We use Google Groups for this purpose. You will be subscribed to the list in the first class. You will not be able to participate fully in the course if you are not subscribed. Make sure you are subscribed with the email address you use most frequently and set your preferences to immediate delivery - "Digest" or "Web only" delivery won't allow you to participate actively in discussions and your participation mark will suffer.
- Coordinator
- Boris Steipe
- Office hours
- I do not hold regular office hours. I prefer communication via e-mail since it leaves you with a document trail of what was discussed, and we can share points of general interest more easily with the class. If you feel you must have a face-to-face meeting, coordinate with me.
- Prerequisites
- Introductory courses to biochemistry and molecular biology provide the contents background to the course. Such might be obtained through the listed prerequistes: BCH210H1/BCH242Y1; BCH311H1/MGY311Y1/PSL350H1[1]; special permission of the course coordinator can be granted.
- It is assumed that students have access to the Internet via their own computer.
- Exclusions & Enrolment controls
- none
- Printed material
- 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. Printing of course material is expressly discouraged since the material is updated frequently.
Recommended textbooks
- Depending on your background, various levels of textbooks may be suitable. I will bring my evaluation copies to class so you can have a look.
- Understanding Bioinformatics (Zvelebil & Baum) is a decent general introduction to many aspects of bioinformatics. It was published in 2007, an updated version is urgently needed. Still, some of the basics (like the algorithm for optimal sequence alignment) don't change. (Amazon) (Indigo) (ABE books)
- Practical Bioinformatics (Agostino) covers some of the material of the BCH441 exercises. Expect a no-nonsense introduction to the very most basic stuff. I have my pet peeves about this book (as I have for many others, eg. why in the world do they still teach CLUSTAL when all available studies demonstrate it to be the least accurate MSA algorithm by a margin???), but if you haven't taken BCH441, this may serve you well. And if you did take BCH441, it may consolidate some ideas that I wasn't clear about. (Amazon) (Indigo) (ABE books)
- If you are aware of recent good textbooks, or have your own opinions about these or other books, let me know.
Grading and Activities
Syllabus and assignments may still undergo changes throughout the term.
| Activity | Weight BCH441 - (Undergraduates) |
Weight BCH1441 - (Graduates) |
| 12 In-class quizzes | 42 marks (12 x 3.5) | 24 marks (12 x 2) |
| Bioinformatics project | 28 marks (5 + 14 + 9) | 28 marks |
| "Classroom" participation | 10 marks | 10 marks |
| Thesis Project | 18 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.
Timetable and syllabus
I n t r o d u c t i o n
| Week | Date | Topics | Activities | Assignment |
| 1 | Sept. 8 - 14 |
Bioinformatics focusses on the data and methods, and Computational Biology defines the objectives, to bring our understanding of Biology to a rigorous, principled, quantitative and predictive level. Over the last two decades, ever since bioinformatics began to take centre stage in the life sciences, the rate of change in the discipline has continuously accelerated. In part, driven by the growth of the Internet, in part through novel algorithms, but to the largest part driven through a very large increase in the volume and quality of data, opportunities for computational analysis in the life science lab have grown in leaps and bounds. One of the associated challenges is to keep abreast of the rapidly changing methods and tools that are available. This course focuses on the basic principles and concepts of the field and emphasis techniques and skills that are easily accessible and freely available to every life science researcher.
|
— | Assignment 1 |
D a t a a n d D a t a A n a l y s i s
| Week | Date | Topics | Activities | Assignment |
| 2 | Sept. 15 - 21 |
In principle, most of the data of interest to us is freely available on the Web, in public repositories. However, the number of databases and associated Web services is large and in constant flux and integrating the data has its own issues. The most important issue is to be clear about the abstractions we use and how they relate back to the biology they describe.
|
Quiz 1 | Assignment 2 |
| 3 | Sept. 22 - 28 |
...
Lecture notes 2014: 04 - Sequence Analysis I (PDF 12.5 MB) |
Quiz 2 | Assignment 3 |
| 4 | Sept. 29 - Oct. 5 |
...
|
Quiz 3, first phase of project due | Assignment 4 |
H o m o l o g y
| Week | Date | Topics | Activities | Assignment |
| 5 | Oct. 6 - 12 |
...
|
Quiz 4 | Assignment 5 |
| 6 | Oct. 13 - 19 |
...
|
Quiz 5 | Assignment 6 |
| 7 | Oct. 20 - 26 |
...
|
Quiz 6 | Assignment 7 |
| 8 | Oct. 27 - Nov. 2 |
...
|
Quiz 7 | Assignment 8 |
G e n o m e s
| Week | Date | Topics | Activities | Assignment |
| 9 | Nov. 3 - 9 |
...
|
Quiz 8 | Assignment 9 |
| 10 | Nov. 10 - 16 |
...
Lecture notes 2014: 18 - Human Genomics (PDF 7.9 MB)
|
Quiz 9, project submission due | Assignment 10 |
P h y l o g e n i e s
| Week | Date | Topics | Activities | Assignment |
| 11 | Nov. 17 - 23 |
...
Lecture notes 2014: 19 - Phylogenetic Analysis I: Principles (PDF 11.5 MB)
|
Quiz 10 | Assignment 11 |
| 12 | Nov. 24 - 30 |
...
Lecture notes 2014: 21 - Function Annotation (PDF 10.1 MB)
|
Quiz 11, project reviews due | Assignment 12 |
| - | Dec. 2 |
...
Previous Exam questions |
Quiz 12 |
Resources
- Course related
- The 2014 Course Google Group.
- The Student Wiki.
- Netiquette for the Group mailing list
- Previous BCH441_Final_Exam
- Contents related
- The UCSF Chimera tutorial
- The Stereo Vision tutorial
- The Aminoacid tutorial
- The Database Identifiers tutorial
- The Introduction to R tutorial
Notes
- ↑ Please check the official Calendar for the academic year to confirm.
