Difference between revisions of "Bioinformatics Main Page"
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BCH441 - Bioinformatics | BCH441 - Bioinformatics | ||
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| − | Welcome to | + | Welcome to BCH441. |
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| − | <small>'''These wiki pages provide information and materials, and coordinate activities and projects in the introductory bioinformatics courses and other workshops taught by Boris Steipe at the University of Toronto'''. If you are not one of my students, you can still browse this site, however I can't provide support for your explorations. The material may be useful if you invest some effort in studying it systematically.</small> | + | <!-- small>'''These wiki pages provide information and materials, and coordinate activities and projects in the introductory bioinformatics courses and other workshops taught by Boris Steipe at the University of Toronto'''. If you are not one of my students, you can still browse this site, however I can't provide support for your explorations. The material may be useful if you invest some effort in studying it systematically.</small --> |
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| + | The link that brought you here is no longer current: | ||
| − | + | * for CSB195 click [http://steipe.biochemistry.utoronto.ca/bio/CSB195-syllabus.html '''here''']. | |
| − | + | * for MGY441 click [http://steipe.biochemistry.utoronto.ca/bio/MGY441-syllabus.html '''here''']. | |
| − | + | </div> | |
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| + | <small>Remember to frequently "pull" from the GitHub repository when you work with the course R-project in RStudio, to load the most recent version of the code, including all patches and additional clarifications</small> | ||
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Welcome! | Welcome! | ||
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| + | Updates to syllabus, marking scheme, and course materials are now in progress. Last year was the first online-only delivery of the course and it actually went really well. But this year will be even better as we'll try a few things that work much better online than in the classroom. Drop me a line if you have any questions, or concerns, or want to share experiences with online classes that went beyond your expectations. | ||
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| + | See you in class! | ||
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__TOC__ | __TOC__ | ||
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| − | BCH441 | + | BCH441 is an introduction to current bioinformatics for life science students and the specialists in the BCB Program. The course provides an overview of the sources of biomolecular data, data annotation and integration, and the interpretation of results through evidence-based reasoning. This includes the ''components'' – sequence, structure, and function, the ''relationships'' in phylogeny and in the networks of interactions and regulation, and the “systems” through which we conceptually organize our knowledge. |
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The emphasis is on practical, hands-on exploration of resources in tasks and assignments. You will improve your general computer literacy and you will learn to use the programming language and statistical workbench '''R'''. Writing your own code has become indispensable in any life-science laboratory. (Yes, you will learn to program.) | The emphasis is on practical, hands-on exploration of resources in tasks and assignments. You will improve your general computer literacy and you will learn to use the programming language and statistical workbench '''R'''. Writing your own code has become indispensable in any life-science laboratory. (Yes, you will learn to program.) | ||
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{{#lst:User:Boris|Instructor}} | {{#lst:User:Boris|Instructor}} | ||
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===Dates=== | ===Dates=== | ||
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For generic dates in the Fall term, see the [https://www.artsci.utoronto.ca/current/dates-deadlines/academic-dates Faculty "Academic Dates" calendar]. For specific due dates, see the [https://q.utoronto.ca/courses/180416/assignments Assignments page on Quercus]. | For generic dates in the Fall term, see the [https://www.artsci.utoronto.ca/current/dates-deadlines/academic-dates Faculty "Academic Dates" calendar]. For specific due dates, see the [https://q.utoronto.ca/courses/180416/assignments Assignments page on Quercus]. | ||
==Contents== | ==Contents== | ||
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This course will be taught in a new format: I have split up the large domain of Bioinformatics into small "learning units" that focus more or less on a single concept. You work through the units independently, in any order that makes sense to you, at your own pace, all with the goal to acquire the knowledge and skills to work on four main "Integrator Units" that bring the contents together. | This course will be taught in a new format: I have split up the large domain of Bioinformatics into small "learning units" that focus more or less on a single concept. You work through the units independently, in any order that makes sense to you, at your own pace, all with the goal to acquire the knowledge and skills to work on four main "Integrator Units" that bring the contents together. | ||
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====Timing and important dates==== | ====Timing and important dates==== | ||
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| − | * Tuesday, September 29. 2020 - First of four learning units due. | + | * Tuesday, September 29. 2020 - First of four learning units due. (Extended to 2020-10-06) |
* Tuesday, October 6. 2020 - Second of four learning units due. | * Tuesday, October 6. 2020 - Second of four learning units due. | ||
* Tuesday, October 13. 2020 - Third of four learning units due. | * Tuesday, October 13. 2020 - Third of four learning units due. | ||
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====Submission of items for marking==== | ====Submission of items for marking==== | ||
| − | Details are listed with each evaluation unit, but in principle you create a separate sub-page of your user page and post your material there. | + | Details are listed with each evaluation unit, but in principle you create a separate sub-page of your user page and post your material there. Then you submit a link to your page on Quercus and I can find the page and mark it. |
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Since most of the learning units include hands-on, practical components that you do on your own, we won't need to us class-time for textbook-like delivery of contents. In class meetings ... | Since most of the learning units include hands-on, practical components that you do on your own, we won't need to us class-time for textbook-like delivery of contents. In class meetings ... | ||
* ... we will always take time for open discussion of topics as they arise. This will be driven by student input and feedback. | * ... we will always take time for open discussion of topics as they arise. This will be driven by student input and feedback. | ||
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* ... I will go over some of the contents details. | * ... I will go over some of the contents details. | ||
* ... I may discuss marking of some submissions I have received, to make the process more transparent. | * ... I may discuss marking of some submissions I have received, to make the process more transparent. | ||
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A breakdown of knowledge that I expect you to acquire outside our course, or bring with you from previous courses, is [[FND-prerequisites|'''listed here''']]. | A breakdown of knowledge that I expect you to acquire outside our course, or bring with you from previous courses, is [[FND-prerequisites|'''listed here''']]. | ||
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Extensions for term work in this course are subject to Faculty regulations and will only be considered within the framework determined by the Faculty policies. | Extensions for term work in this course are subject to Faculty regulations and will only be considered within the framework determined by the Faculty policies. | ||
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* '''Submissions due before the {{DropdateFall}}.''' | * '''Submissions due before the {{DropdateFall}}.''' | ||
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* '''Signing up for the oral tests.''' | * '''Signing up for the oral tests.''' | ||
| − | ::The dates for the oral tests are in two weeks '''after''' the Drop Date. If you fail to | + | ::The dates for the oral tests are in two weeks '''after''' the Drop Date. If you fail to connect to the Zoom meeting at the scheduled time, this is equivalent to a missed midterm exam in terms of applicable Faculty policy: "if the reasons for missing your test are ''acceptable'' to the instructor, a make-up opportunity should be offered to the student where ''practicable''. '''"Acceptable"''' reasons will be considered if they are justified, if the consideration is "fair, equitable and reasonable", and if the reason is documented through one of the four types of "official" documentation: UofT Verification of Illness or Injury Form, Student Health or Disability Related Certificate, a College Registrar’s Letter, and an Accessibility Services Letter. Scope for a '''"practicable"''' make-up opportunity for the oral test will be extremely limited however. |
* '''Submissions due on the {{LastdateFall}}.''' | * '''Submissions due on the {{LastdateFall}}.''' | ||
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*The [http://steipe.biochemistry.utoronto.ca/abc/students '''Student Wiki'''] | *The [http://steipe.biochemistry.utoronto.ca/abc/students '''Student Wiki'''] | ||
*[http://www.writing.utoronto.ca/advice '''Writing advice'''] from the UofT Writing Centre <small>(including: how to avoid plagiarism)</small> | *[http://www.writing.utoronto.ca/advice '''Writing advice'''] from the UofT Writing Centre <small>(including: how to avoid plagiarism)</small> | ||
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| + | [[Category:Bioinformatics]] | ||
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