Difference between revisions of "Bioinformatics Main Page"
Jump to navigation
Jump to search
m |
m |
||
(38 intermediate revisions by the same user not shown) | |||
Line 1: | Line 1: | ||
<div id="BIO"> | <div id="BIO"> | ||
− | <div class="b1"> | + | <!-- div class="b1"> |
BCH441 - Bioinformatics | BCH441 - Bioinformatics | ||
<div style="font-size:50%;font-weight:normal;"> | <div style="font-size:50%;font-weight:normal;"> | ||
− | Welcome to | + | Welcome to BCH441. |
− | |||
</div> | </div> | ||
+ | </div --> | ||
− | <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 --> |
+ | <div class="alert"> | ||
+ | The link that brought you here is no longer current: | ||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> | ||
<!-- | <!-- | ||
+ | <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> | ||
+ | |||
Welcome! | Welcome! | ||
Line 22: | Line 28: | ||
(17:00, BA1190) --> | (17:00, BA1190) --> | ||
+ | |||
+ | <!-- | ||
</div> | </div> | ||
+ | {{Smallvspace}} | ||
+ | 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. | ||
+ | See you in class! | ||
+ | {{Vspace}} | ||
+ | --> | ||
+ | |||
+ | <!-- div class="ToDo"> | ||
+ | * <strike>upgrade MediaWiki to the newest version for the Course Wiki and the Student wiki</strike> | ||
+ | * <strike>re-code the API mechanism for uploads</strike> | ||
+ | * Configure [https://q.utoronto.ca/courses/180416 Quercus course page:] | ||
+ | ** <strike>Add a discussion section</strike> | ||
+ | ** Figure out Bb Collaborate principles | ||
+ | *** What is the "Course Room" best used for? | ||
+ | *** What are the "Sessions" best used for? | ||
+ | *** <strike>Can we make lecture recordings? Where can we store them? How can they be accessed?</strike> | ||
+ | * <strike>Is there a mailing list?</strike> <small>Doesn't look like it, use the Discussion module instead.</small> | ||
+ | * Decide on evaluations and marking scheme | ||
+ | * <strike>Explore bulk student registration for the Student Wiki</strike> | ||
+ | * Update Student Wiki resources | ||
+ | * Decide on scheduling | ||
+ | ** Schedule oral tests | ||
+ | * Update Syllabus page | ||
+ | * Update course materials | ||
+ | ** Begin conversion to <code>.Rmd</code> | ||
+ | </div --> | ||
+ | |||
+ | <!-- BLANK EVERYTHING ! | ||
__TOC__ | __TOC__ | ||
Line 34: | Line 69: | ||
{{Smallvspace}} | {{Smallvspace}} | ||
− | 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. |
Line 49: | Line 84: | ||
* introduction to systems-level concepts. | * introduction to systems-level concepts. | ||
− | + | 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.) | |
− | |||
− | |||
− | |||
− | |||
− | |||
Line 61: | Line 91: | ||
===Dates=== | ===Dates=== | ||
− | + | {{Smallvspace}} | |
+ | |||
− | + | 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== | ||
− | + | {{Smallvspace}} | |
− | + | 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. | |
+ | Through this, the course accommodates different levels of preparation more flexibly, probably makes your work more efficient, and implicitly teaches a number of meta-skills such as reporting and time-management. Be mindful though: this format requires a high level of self-motivation and responsibility to do well. You will frequently be on your own - just like you are in "real life". But since you are the best judge of what is easy or hard for you, you can use your time very efficiently, gloss over familiar things and play and explore with contents that you enjoy. | ||
{{Vspace}} | {{Vspace}} | ||
Line 80: | Line 111: | ||
{{Vspace}} | {{Vspace}} | ||
− | This course comprises | + | This course comprises three key, integrative activities and preparatory "learning units" that lead up to them. Learning units can be completed in any sequence that makes sense to you, at any time until the deadline to submit material. You can find the detailed due dates on [https://q.utoronto.ca/courses/180416 ''Quercus'']. Note that scheduling your oral test needs to be done in advance. |
There are also a few restrictions on which units you must complete within this course: | There are also a few restrictions on which units you must complete within this course: | ||
− | * you must complete | + | * you must complete three of four <span style="background-color: #e19fa7; border:solid 2px #000000;"> Integrator Units </span> and submit them for marking. These will be worth maximally 50 marks ((2 x 13) + (1 x 24)); 24 marks are available for the unit that you choose for your oral test; |
− | |||
− | |||
− | * | + | * you can submit up to four other <span style="background-color: #b3dbce; border:solid 2px #000000;"> learning units </span> worth up to an additional 20 marks for marking. These units are worth 5 marks each. There are a number of units available, which ones you choose is up to you. |
− | * 25% of your mark will be | + | * 25% of your mark will be earned with your [[FND-Journal|'''Course Journal''']] at the end of class. |
− | * 5% of your mark will be | + | * 5% of your mark will be earned with your [[ABC-Insights|'''insights!''' page]] at the end of class. |
Please carefully read the [[ABC-Rubrics|'''evaluation rubrics''']] for each category of deliverables. | Please carefully read the [[ABC-Rubrics|'''evaluation rubrics''']] for each category of deliverables. | ||
− | |||
− | |||
− | |||
{{Vspace}} | {{Vspace}} | ||
Line 105: | Line 131: | ||
<tr class="sh"> | <tr class="sh"> | ||
<td><b>Activity</b></td> | <td><b>Activity</b></td> | ||
− | <td><b>Weight</b | + | <td><b>Weight</b></td> |
− | |||
</tr> | </tr> | ||
− | <tr><td colspan=" | + | <tr><td colspan="2" class="sp"></td></tr> |
<tr class="s2"> | <tr class="s2"> | ||
− | <td>Integrator Units</td> | + | <td>Three Integrator Units</td> |
− | <td> | + | <td>50 marks (2*13 + 1*24)</td> |
− | |||
</tr> | </tr> | ||
<tr class="s1"> | <tr class="s1"> | ||
− | <td> | + | <td>Four other learning units</td> |
− | <td> | + | <td>20 marks (4*5)</td> |
− | |||
</tr> | </tr> | ||
<tr class="s2"> | <tr class="s2"> | ||
<td>Course Journals</td> | <td>Course Journals</td> | ||
− | |||
<td>25 marks</td> | <td>25 marks</td> | ||
</tr> | </tr> | ||
Line 131: | Line 153: | ||
<tr class="s1"> | <tr class="s1"> | ||
<td>insights! page</td> | <td>insights! page</td> | ||
− | |||
<td>5 marks</td> | <td>5 marks</td> | ||
</tr> | </tr> | ||
+ | |||
+ | <tr><td colspan="2" class="sp"></td></tr> | ||
<tr class="s2"> | <tr class="s2"> | ||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
<td>'''Total'''</td> | <td>'''Total'''</td> | ||
− | |||
<td>100 marks</td> | <td>100 marks</td> | ||
</tr> | </tr> | ||
Line 153: | Line 167: | ||
;A mix of evaluation methods | ;A mix of evaluation methods | ||
− | :'''Learning units''' will be evaluated with a mix of approaches including technical reports, documentation of results in your journal, delivery of R code | + | :'''Learning units''' will be evaluated with a mix of approaches including technical reports, documentation of results in your journal, delivery of R code, ... Details will be described in the individual units. You will be required to submit evaluations in different categories. |
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
{{Vspace}} | {{Vspace}} | ||
− | :'''Integrator units''' will be evaluated with a mix of approaches including technical reports, delivery of R code, and oral tests. Technical reports, R code and other options will be worth | + | :'''Integrator units''' will be evaluated with a mix of approaches including technical reports, delivery of R code, and oral tests. Technical reports, R code and other options will be worth 10 marks each, the oral test will be worth 20 marks. You can submit at most one of each evaluation category (and one of your evaluations must be an oral test). Also, your oral test can not be your first evaluation, and the topics will be cumulative. Details will be described in the individual units. |
− | ::'''Oral tests for Integrator Units''' will be scheduled | + | ::'''Oral tests for Integrator Units''' will be scheduled from mid-November to early December in the afternoon. Details can be found on the sign-up page that is linked from the resp. integrator units. |
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
+ | <small> | ||
+ | I do not adjust marks towards a target mean and variance (i.e. there will be no "belling" of grades), but I follow the principles laid out in the marking rubrics. "Normalization" of grade interferes with 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 bring down your own mark. Collaborate as much as possible, it is a great way to learn. | ||
+ | But take *utmost* care to follow the instructions on avoiding [[ABC-Plagiarism|'''plagiarism and academic misconduct''']] to the letter, they will be rigorously enforced.</small> | ||
{{Vspace}} | {{Vspace}} | ||
Line 187: | Line 187: | ||
Here is a '''thematic overview''' of the topical areas of this course's learning units: | Here is a '''thematic overview''' of the topical areas of this course's learning units: | ||
− | [[File:ABC-Units_landscape. | + | [[File:ABC-Units_landscape.svg|thumb|500px|none|link=http://steipe.biochemistry.utoronto.ca/abc/images/b/b0/ABC-Units_landscape.svg|'''The bioinformatics learning unit landscape.''']] |
− | |||
Line 195: | Line 194: | ||
* <command>-Click to open the Learning Units Map in a new tab, scale for detail. | * <command>-Click to open the Learning Units Map in a new tab, scale for detail. | ||
− | [[File:ABC-units_map.svg|thumb|500px|none|link=http://steipe.biochemistry.utoronto.ca/abc/ | + | [[File:ABC-units_map.svg|thumb|500px|none|link=http://steipe.biochemistry.utoronto.ca/abc/images/a/ae/ABC-units_map.svg|'''A clickable map of the bioinformatics learning units.''']] |
+ | |||
+ | |||
* Hover over a learning unit to see its keywords. | * Hover over a learning unit to see its keywords. | ||
* Click on a learning unit to open the associated page. | * Click on a learning unit to open the associated page. | ||
Line 224: | Line 225: | ||
*[[ABC-Insights|The "insights!" page]] | *[[ABC-Insights|The "insights!" page]] | ||
:{{#lst:ABC-Insights|abstract}} | :{{#lst:ABC-Insights|abstract}} | ||
− | |||
Line 289: | Line 289: | ||
<tr> | <tr> | ||
− | <td> | + | <td> She is done with her deliverables mid November. So she completes the [[ABC-INT-Genome_annotation|genome annotation Integrator Unit]] to learn on her own. She fill in the rest of the database units, the units on statistics and analysis of differential expression in genes, the units on networks and protein-protein interactions, and the concepts of protein functions, to complete the [[BIN-FUNC-Annotation]] milestone, ... |
</td> | </td> | ||
<td>[[File:ABC-Scenario-1-Step-7.jpg|thumb|300px|none|link=http://steipe.biochemistry.utoronto.ca/abc/assets/ABC-Scenario-1-Step-7.jpg]]</td> | <td>[[File:ABC-Scenario-1-Step-7.jpg|thumb|300px|none|link=http://steipe.biochemistry.utoronto.ca/abc/assets/ABC-Scenario-1-Step-7.jpg]]</td> | ||
Line 300: | Line 300: | ||
<tr> | <tr> | ||
− | <td>And that's it | + | <td>And that's it. </td> |
<td>[[File:ABC-Scenario-1-Step-final.jpg|thumb|300px|none|link=http://steipe.biochemistry.utoronto.ca/abc/assets/ABC-Scenario-1-Step-final.jpg]]</td> | <td>[[File:ABC-Scenario-1-Step-final.jpg|thumb|300px|none|link=http://steipe.biochemistry.utoronto.ca/abc/assets/ABC-Scenario-1-Step-final.jpg]]</td> | ||
</tr> | </tr> | ||
Line 310: | Line 310: | ||
</div> | </div> | ||
− | |||
− | |||
− | |||
{{Smallvspace}} | {{Smallvspace}} | ||
Line 332: | Line 329: | ||
* Next, he realizes that much of what he has worked with so far has implicitly relied on sequence-alignment tools. So he completes the alignment cluster next (Bin-ALI-...). | * Next, he realizes that much of what he has worked with so far has implicitly relied on sequence-alignment tools. So he completes the alignment cluster next (Bin-ALI-...). | ||
* And realizing that multiple sequence alignments ([[BIN-ALI-MSA]]) are fundamental to phylogenetic analysis leads him to tackle the phylogenetic analysis cluster next (BIN-PHYLO-...). | * And realizing that multiple sequence alignments ([[BIN-ALI-MSA]]) are fundamental to phylogenetic analysis leads him to tackle the phylogenetic analysis cluster next (BIN-PHYLO-...). | ||
− | * That's it for the learning units. Nigel then completes | + | * That's it for the learning units. Nigel then completes all Integrator Units one after another except for the Homology modelling one; he starts with the [[ABC-INT-Genome_annotation|genome annotation unit]] because that's the biggest one and he wants it safely submitted before the end-of-term rush in his other courses gets to him. |
Line 340: | Line 337: | ||
{{Vspace}} | {{Vspace}} | ||
− | |||
− | + | ====Timing and important dates==== | |
− | + | Having students work through the material entirely at their own pace has had limited success. A minority did very well, but the majority found themselves quite stressed out towards the end of the term. Thus we will proceed with a structured sequence of due dates that spreads the deliverables evenly. However: a due date is the '''last''' date on which assignments are due, and you can submit your assignments much, much sooner and relax towards the end of the term. | |
− | + | You can work through the material at your own pace. Non-negotiable restrictions arise from the {{DropdateFall}}, and that everything needs to be done by the {{LastdateFall}}: | |
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | You can work through the material | ||
− | |||
− | |||
{{Vspace}} | {{Vspace}} | ||
− | * Tuesday, September | + | * Tuesday, September 29. 2020 - First of four learning units due. (Extended to 2020-10-06) |
− | * Tuesday, October | + | * Tuesday, October 6. 2020 - Second of four learning units due. |
− | * Tuesday, October | + | * Tuesday, October 13. 2020 - Third of four learning units due. |
− | * | + | * Tuesday, October 20. 2020 - Last of four learning units due. |
− | + | * '''November 9-13 - Fall Reading Week''' | |
− | * November | + | * Monday, November 9. 2020 - Drop Date, and first Integrator unit due. |
− | * | + | * Monday, November 16 to Friday, November 27. 2020 - Oral Tests. Second Integrator Unit due on the day before the test. |
− | * | + | * Tuesday, December 8. 2020 - All remaining submissions due |
− | * Tuesday, December | ||
− | |||
− | |||
− | |||
{{Vspace}} | {{Vspace}} | ||
Line 376: | Line 359: | ||
====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. |
{{Vspace}} | {{Vspace}} | ||
Line 382: | Line 365: | ||
====Class time==== | ====Class time==== | ||
− | 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. | + | 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. |
− | * | + | * ... I will go over some of the contents details. |
− | * I | + | * ... I may discuss marking of some submissions I have received, to make the process more transparent. |
− | |||
− | |||
+ | Class sessions will be recorded and posted. | ||
{{Vspace}} | {{Vspace}} | ||
Line 395: | Line 377: | ||
{{Vspace}} | {{Vspace}} | ||
− | |||
− | |||
− | |||
Line 406: | Line 385: | ||
===Prerequisites=== | ===Prerequisites=== | ||
− | Introductory courses to biochemistry and molecular biology provide the contents background to the course. Such might be obtained through the listed prerequiste courses: BCH210H1/BCH242Y1; BCH311H1/MGY311Y1/PSL350H1<ref>Please check the [ | + | Introductory courses to biochemistry and molecular biology provide the contents background to the course. Such might be obtained through the listed prerequiste courses: BCH210H1/BCH242Y1; BCH311H1/MGY311Y1/PSL350H1<ref>Please check the [https://fas.calendar.utoronto.ca/course/bch441h1 '''official Calendar'''] for the academic year to confirm the "official" prerequisites.</ref>. However I have no way to assess your success in these courses, nor do I know what material actually '''was''' covered. Thus, I generally waive prerequisites. In all cases it is your responsibility to be sufficiently prepared and to make up for material that you have not covered previously. |
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''']]. | ||
− | |||
− | |||
{{Vspace}} | {{Vspace}} | ||
Line 417: | Line 394: | ||
{{Smallvspace}} | {{Smallvspace}} | ||
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. | ||
− | |||
− | |||
* '''Submissions due before the {{DropdateFall}}.''' | * '''Submissions due before the {{DropdateFall}}.''' | ||
Line 424: | Line 399: | ||
* '''Signing up for the oral tests.''' | * '''Signing up for the oral tests.''' | ||
− | ::The dates for the oral tests | + | ::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}}.''' | ||
Line 450: | Line 425: | ||
;Course related | ;Course related | ||
− | *The [ | + | *The [https://q.utoronto.ca/courses/180416 '''Quercus course page'''] |
*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> | ||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
{{Vspace}} | {{Vspace}} | ||
− | |||
− | |||
− | |||
− | |||
===Notes=== | ===Notes=== | ||
<references /> | <references /> | ||
+ | [[Category:Bioinformatics]] | ||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
--> | --> | ||
− | |||
− | |||
− |