Difference between revisions of "Bioinformatics Main Page"

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BCH441 - Bioinformatics
 
BCH441 - Bioinformatics
  
 
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Welcome to the "Course Wiki" for BCH441 / BCH1441.
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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>
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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 -->
  
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The link that brought you here is no longer current:
  
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*  for CSB195 click [http://steipe.biochemistry.utoronto.ca/bio/CSB195-syllabus.html '''here'''].
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BCH441 will reconvene in the fall term of 2020. It will be delivered in an online only mode. Visit this page in early September for details.
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*  for MGY441 click [http://steipe.biochemistry.utoronto.ca/bio/MGY441-syllabus.html '''here'''].
  
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First online class session: Tuesday, September 15. @ 17:00. <small>(Probably)</small>
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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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* <strike>upgrade MediaWiki to the newest version for the Course Wiki and the Student wiki</strike>
 
* <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>
 
* <strike>re-code the API mechanism for uploads</strike>
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* Update course materials
 
* Update course materials
 
** Begin conversion to <code>.Rmd</code>
 
** Begin conversion to <code>.Rmd</code>
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__TOC__
 
__TOC__
  
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BCH441 (BCH1441) 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.  
+
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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* introduction to systems-level concepts.
 
* introduction to systems-level concepts.
  
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Practical, hands on tasks and assignments will introduce public data resources and analysis tools. Along with improving general computer literacy, you will learn to use the programming language and statistical workbench '''R''', with a special emphasis on the kind of everyday tasks of data preparation and analysis that have become indispensable for 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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−
The course is complemented by [[Computational_Systems_Biology_Main_Page|'''BCB420&nbsp;/&nbsp;JTB2020''']] (offered in the Winter Term) which consolidates aspects of computational systems biology in a project context.
 
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<code>BCH441H1F</code> is the undergraduate course code.<br>
 
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<code>BCH1441H1F</code> is the cross-listed course code for graduate students.
 
  
  
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===Dates===
 
===Dates===
  
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BCH441 is a Fall Term course. We will hold interactive online sessions Tuesdays, 17:00 to 20:00 (though it is unlikely that we will take the full three hours).
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;First online meeting – Tuesday, September 15.
 
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:We will go over the course delivery and organizational details, and this is crucial information to get you off to a running start.
 
  
 
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].
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==Contents==
 
==Contents==
  
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This course will be taught in a new format: the domain of Bioinformatics has been decomposed into small "learning units" that are focussed 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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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. In terms of aiming for the highest level of understanding and competence, you will frequently be on your own - just like you are in "real life". On the other hand, you certainly are the best judge of how well prepared you are. Thus there should be no surprises when your deliverables are evaluated.
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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.
  
 +
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.
  
 
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:'''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.
 
:'''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.
  
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::'''Oral tests for Integrator Units''' will be scheduled from mid-November to early December in the afternoon. Please refer to the sign-up page (linked from the resp. integrator units) for details.
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::'''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.
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<div class="toccolours mw-collapsible mw-collapsed" style="width:800px">
 
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'''A final note on marking policy...'''
 
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<div class="mw-collapsible-content">
 
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I do not adjust marks towards a target mean and variance (i.e. there will be no "belling" of grades), but follow the principles laid out in the marking rubrics. I feel strongly that "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 have the effect that it brings down your mark because the class average is "belled-down" by the instructor. Collaborate as much as possible, it is a great way to learn.
 
−
 
 
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<small>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>
 
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−
</div>
 
−
</div>
 
  
  
 +
<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>
  
 
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*[[ABC-Insights|The "insights!" page]]
 
*[[ABC-Insights|The "insights!" page]]
 
:{{#lst:ABC-Insights|abstract}}
 
:{{#lst:ABC-Insights|abstract}}
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<td>Finally, as a kind of capstone, she completes the [[ABC-INT-Genome_annotation|genome annotation Integrator Unit]]. So 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, ...
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<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>
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<td>And that's it. Units she hasn't covered were optional.</td>
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<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>
 
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* 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 the four Integrator Units one after another, starting 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.
+
* 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.
  
  
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====Timing and important dates====
  
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<!-- We will work through an integrator unit in class; this is a new unit that is itself not submitted for evaluation but is meant to model the process of translating concepts to requirements, requirements to tasks, and bringing a project to a defined conclusion, all supported by the ABC knowledge network.
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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.
  
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* Access the [[ABC-INT-GO_categories|'''GO term categories''' unit here]].
+
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}}:
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* <small>Access a series of posts about progress with solving the [http://steipe.biochemistry.utoronto.ca/abc/students/index.php/User:Boris/BCH441-2018_GOTerm_project '''GO term categories''' challenge here].</small>
 
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====Timing and important dates====
 
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You can work through the material entirely at your own pace. There are only two restrictions: a minimum amount of evaluations have to be submitted and marked before the {{DropdateFall}}, and everything needs to be done by the {{LastdateFall}}:
 
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* Work from learning units worth at least 10% of your final grade must have been submitted for evaluation by October 31, so that I can mark it before the {{DropdateFall}}. If you have not submitted enough work for evaluation by October 31, I will randomly choose an appropriate number of learning units and record a 0 for these.
 
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* All '''remaining course work''' must have been submitted by the {{LastdateFall}}. At least one of the Integrator Units will be evaluated in an oral test and there is a limited number of test-dates.
 
  
 
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* Tuesday, September 10. 2019 - First class - mandatory attendance.
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* Tuesday, September 29. 2020 - First of four learning units due. (Extended to 2020-10-06)
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* Tuesday, October 8. 2018 - Quiz option: [[BIN-NCBI]], [[BIN-EBI]]
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* Tuesday, October 6. 2020 - Second of four learning units due.
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* Tuesday, October 22. 2018 - Quiz option: [[FND-MAT-Graphs_and_networks]]
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* Tuesday, October 13. 2020 - Third of four learning units due.
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* Wednesday, October 30 2018: at least 10 marks worth of material has to have been submitted for evaluation
+
* Tuesday, October 20. 2020 - Last of four learning units due.
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* {{DropdateFall}}
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* '''November 9-13 - Fall Reading Week'''
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* November 4-8 - Fall Reading Week
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* Monday, November 9. 2020 - Drop Date, and first Integrator unit due.
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* Tuesday, November 12. 2018 - Quiz option: [[BIN-PPI-Analysis]]
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* Monday, November 16 to Friday, November 27. 2020 - Oral Tests. Second Integrator Unit due on the day before the test.
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* Tuesday, November 26. 2018 - Quiz option: [[BIN-ALI-MSA]]
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* Tuesday, December 8. 2020 - All remaining submissions due
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* Tuesday, December 3. 2018 - No class meeting
 
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* {{LastdateFall}}
 
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====Submission of items for marking====
 
====Submission of items for marking====
  
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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. You add an appropriate category tag to the page when it is ready to be evaluated and I can then easily find and mark your page.
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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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====Class time====
 
====Class time====
  
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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.There will be four main activities in class meetings:
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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 ...
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* 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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* ... 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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* We will jointly work on a designated integrator task: the [[ABC-INT-GO_categories|'''GO term categories''' unit]].
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* ... I will go over some of the contents details.
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* I will discuss marking of some submissions I have received, to make the process more transparent.
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* ... I may discuss marking of some submissions I have received, to make the process more transparent.
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* Some evaluations will include quizzes or presentations. These will happen in class on our dedicated "evaluation days".
 
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* We will organize conversations with scientists in the field – "''Bioinformatics Investigator Chats''" – who will talk about aspects of their own work that are related to the course contents, e.g. how did this database or that algorithm contribute to solve a real problem in the lab. This will provide you with some sense about how the material is meaningful in the real world.
 
  
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Class sessions will be recorded and posted.
  
 
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===Location===
 
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:[http://map.utoronto.ca/utsg/building/080 BA&nbsp;1190] (Bahen Building)
 
  
  
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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''']].
−
 
−
You must have access to the Internet via your own computer. From time to time it may be necessary to bring your computer to class. If you do not have a laptop computer that is set up to work in the University's wireless network, contact me so we can figure out how to work around any issues.
 
  
 
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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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−
<!-- cf. http://www.artsci.utoronto.ca/faculty-staff/teacher-info/academic-handbook-for-instructors/sections-6-8 -->
 
  
 
* '''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.'''
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::The dates for the oral tests have been announced at the beginning of the term. If you fail to sign up for a slot, or if you fail to show up 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.
+
::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>
−
 
−
<!--
 
−
;Contents related
 
−
*<small>Previous [[BCH441_Final_Exam|Final Exams]] (maybe less relevant since the format has changed in 2013)</small>
 
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*The [[UCSF Chimera]] tutorial
 
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*The [[Stereo Vision]] tutorial
 
−
*The [[Aminoacid tutorial]]
 
−
*The [[Database Identifiers]] tutorial
 
−
*The [[R tutorial|Introduction to '''R''']] tutorial
 
−
 
−
*[http://www.ncbi.nlm.nih.gov/books/NBK143764/ The '''NCBI Handbook''']
 
−
*[http://metadatabase.org/ MetaDatabase]
 
−
*[http://nar.oxfordjournals.org/content/44/D1.toc NAR January-2016 '''Database''' issue]
 
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*[http://nar.oxfordjournals.org/content/44/W1.toc NAR July-2016 '''Web server''' issue]
 
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&nbsp;<br>
 
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===Notes===
 
===Notes===
 
<references />
 
<references />
  
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[[Category:Bioinformatics]]
  
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&nbsp;<br>
 
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[[Category:Bioinformatics]]
 
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Latest revision as of 03:31, 19 September 2022


The link that brought you here is no longer current:

  • for CSB195 click here.
  • for MGY441 click here.



Retrieved from "http://steipe.biochemistry.utoronto.ca/abc/index.php?title=Bioinformatics_Main_Page&oldid=11979"