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The resources linked from this page contain information, and coordinate activities in courses and workshops taught by Boris Steipe and colleagues. If you are not one of our currently enrolled students, we cannot provide support for your explorations. However you are free to follow the links and the material may be useful if you invest effort in studying it systematically.

Welcome …

This is the new MGY441 syllabus for 2022, the bioinformatics course that was previously taught as BCH441. I’m very excited to welcome a TA to the course for the first time in years, and two colleagues as co-instructors. We expect that the material we will cover in our in-class sessions will fluidly focus on current developments and trends in the field, while the backbone of contents will come from online learning units and R code in an “inverted course” model. See below for details.

See you “in class” !

 

The Course

MGY441 is an introduction to the field of bioinformatics taught with the R programming language. Boris Steipe is the main course instructor and has designed the course to emphasize hands-on skills and knowledge that will be useful in many ways beyond the classroom. Jesse Gillis and Jared Simpson will provide additional perspectives on the field. Our TA Justin Sing will work primarily to provide formative feedback to enhance your learning experience. This is in principle an “inverted” course, and the in-class components will be taught online. The majority of work will be at your own pace, outside the classroom.

The course topics

MGY441 introduces the concepts and practice of bioinformatics; it is aimed at life science students, in particular in the MGY Programs, and the specialists in the BCB Program - but it may be useful much more broadly. 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 that underly phylogenies and from which the networks of protein interaction and gene regulation can be constructed, and the “systems” , through which we conceptually organize our knowledge.

The course topics include …

Outcomes

I emphasize practical, hands-on exploration of resources in tasks and assignments. You will learn the key concepts of the field to the degree that you will be able to continue in this field on your own, you will improve your general computer literacy, and you will learn to read and write code in the programming language R. Writing your own code has become indispensable in any life-science laboratory, so, yes, you will learn to program.

Instructors

TA

Justin Sing <justinc.sing@mail.utoronto.ca>

Locations

There are five main locations where the course will play out:

  1. Most learning material is in HTML pages on this server.
  2. Programming tasks are based on two RStudio projects that live on GitHub: there is a “basic setup” project, as a first introduction, and the crucial ABC-Units project which you install with instructions in the “RPR-Introduction” unit. That project forms the core of the course activities. All programing will be done on your own computer and all the tools you work with can become part of your future graduate work.
  3. All material that is submitted by you for credit will be on your own Google doc pages. You should set up a folder there that contains an introductory “User” page, your assignments, and your “Lab Journal”.1 You will need a Google account for this and if you do not have one, you will need to create one for this course.
  4. The course page on Quercus is our hub for course-administration mechanics; we will also make good use of the Discussion Board.
  5. Finally, Zoom will provide our classroom. Each week’s URL for our Zoom meetings will be announced via Quercus, a few minutes before the meeting begins.

Dates and Time

For generic dates in the Fall term, see the Faculty “Academic Dates” in the calendar. An important date is the last day to cancel Fall Term courses, and the class-end date for the term. Our assignment due dates are defined with respect to these two cornerstones. For specific due dates, see the Assignments page on Quercus.

Our first class meeting will be on Tuesday, September 13. We will go over the scope and organization of the course. It is really important for you to attend this first meeting and it will be difficult to get you on track if you miss it. Make sure you are enrolled in time to be able to receive the announcement about the meeting with the correct Zoom link via Quercus.2

Our regular meetings will be Tuesdays from 17:10 to 20:00 (for two hours of class and one tutorial). Do keep your calendar open for the entire block, there will be no lecture recordings: you actually need to be there, at the time, to participate.

In-class and at-home

Expect to spend the majority of your time on at-home readings and tasks, then participate in-class to enrich this and add context. We build our learners’ community in-class, and that is an important part of your engagement and learning success, it helps you build a sound scaffold of concepts; you acquire your knowledge and skills at-home, at your own pace, and the details then come together in the scaffold you build in-class. Both parts need to complement each other.

Contents

MGY441 is taught in an online classroom, and learned from navigating a network of interconnected “Learning Units”. A Learning Map provides access to the nodes of the knowledge network. Marked assessments include submitted tasks – some smaller, some more involved; an Oral Test; keeping a Course Journal; participation in asking and answering questions; and recording some meaningful insights on your learning progress.

Why program? Why “R”?

Learning to Program

Why program in the first place? There are two reasons. One is: programming encourages a particular way to think about the world and its problems – computational thinking – that is structured, clear, and effective. It manifests much of what we appreciate about science: reproducibility, transparency, plurality and the like, and we can have some confidence that we understand a concept if we can teach even a computer to process it. The other reason is, as scientists we need to create, not just consume. Once we have solved a problem, we can’t just repeat the same thing over and over again. Unless we construct our own tools, we will not be able to do that. In a landscape in which we strive to push the boundaries, we must have things work together exactly as we need them to, and we need to be able to change them quickly when our needs change. Only the ability to program our own solutions gives us that kind of power.

Mind you, we are not aiming to become “programmers” – we are here to solve problems. Programming helps us to do that. And programming well helps us to do that well.

Choosing R

R is less frequently used than many other languages.3 Is it worth the effort to learn? Programming in practice needs a language that expresses your problem domain well, that is well supported by code composition tools, that makes it easy to integrate others’ code, and that has a large user-base to ensure ongoing adoption and development. It turns out that most computational work in life-science labs requires either Python or R. And since Python is the standard these days for introductory programming courses at school and in university, we complement this with learning R in this course. Actually, I think you can probably get by without Python, but not without R;4. What we will use in this course is a deliberately un-idiomatic dialect of R: simple, predictable constructs that are easy to analyse and maintain, that flatten the learning curve, and that translate without too much trouble into other languages. I trust you will find this approach surprisingly accessible, and remarkably empowering.

But I have never programmed before …

I think that this course is suitable for absolute newcomers. At least some past students had minimal or no prior programming experience, and some of those did really well. I have tried to structure the code samples so they are easy to understand, the flow is transparent, and it is easy to inspect values and debug problems, and I try not to make assumptions about what you know. So I think that a lack of prior experience is not an insurmountable problem, and that this course might actually allow you to fill a major gap in your skill set. Research has shown that it an aptitude to learning natural languages is actually more important than “numeracy” in this regard (Prat et al. 2020). But, there’s a but. Maybe there is a reason for why you had no prior experience: you just don’t like computers, or structured, detail-oriented approaches to problems are just not for you. That’s something you will need to solve. But if it’s just a lack of opportunity, and you’re looking forward to work hard on something new, then I am confident you will do well.

The Course “World of Knowledge”

Open World Format

This course is taught in a unique format that I first developed in 2017: it is an “inverted” course format, for a non-sequential mode of learning. The inverted model frees up valuable contact-time to focus on the interpersonal aspects of learning: figuring out what’s hard, and why, growing a sense of what’s important, building a community of learners. As for the cognitive contents, I have split up the large domain of bioinformatics into small Learning Units that each focus more or less on a single concept. You work through the units independently, in any order that makes sense to you, with the goal to acquire the knowledge and skills to work on the main Integrator Units that bring the contents together. This is an open world of learning, for you to explore at your own pace; the Learning Units are the quests and the Integrators are the final levels.

Through this, we can accommodate different levels of preparation, because you can skip things you don’t need, we can make the work more efficient, because you can avoid redundant contents, and we acquire “meta-skills” such as reporting and time-management. However, there is a catch: this format requires a high level of self-motivation and responsibility to do well. It is a profoundly adult approach and you will frequently be on your own – just like you are in “real life”. But since you are the best judge of your capabilities, you can use your judgement to play and explore what you enjoy. And if you need help, no worries: I’m here.

The Learning Map

Here is a thematic overview of the topical areas we cover in the course:

Bioinformatics – topical areas. Click on the image to load it in a new tab.

Bioinformatics – topical areas. Click on the image to load it in a new tab.

A Map of the Field

… but the key guide through the course is the detailed Learning Map. There are many nodes, if I would print them all out on paper, the material would fill a pretty decent-sized text-book. And that’s how you should approach it – you don’t necessarily ingest everything from the first to the last page, but you study what you need to solve a quest. You can also think of this as an open-world adventure in which there are many sequences of quests that will lead you to a goal.

The Learning Map is the most important asset for this course. Click to load. Then bookmark, scale and study. Nodes are linked to study material, shaded fields provide approximate guidance in which week of the course (I–XII) the material will be assumed known, but students are encouraged to find their own path through the network and to work at their own speed.

The Learning Map is the most important asset for this course. Click to load. Then bookmark, scale and study. Nodes are linked to study material, shaded fields provide approximate guidance in which week of the course (I–XII) the material will be assumed known, but students are encouraged to find their own path through the network and to work at their own speed.

Load this map and scale it so you can read the labels. Note the icons that link to resources at the top left. Each node in the network is linked to a page for a Learning Unit. Hover over a learning unit to see its keywords. Click on a Learning Unit node to open the linked page. The nodes are colour-coded:

Map Colour-Codes

  •   Live units   are green
  •   Units under development   are light green. These are still in progress.
  •   Stubs   (placeholders) are pale. These still need basic contents.
  •   Milestone units   are blue. These collect a number of preparatory units to simplify the network.
  •   Integrator units   are red. These embody the main goals of the course and contain tasks that can be delivered for credit.
  •   Units that need revision  before they should be studied are pale orange.

Learning Units with a   black border   have deliverables that can be submitted for formative feedback. See the marking scheme for details.

Arrows point from a preparatory unit to a unit that assumes it has been studied.

Activities and Grading

For many, the final marks are the most important part of a course. However, I hope that for you it is actually the learning experience that counts most: how interesting and useful the material is, how it encourages you to grow as a scholar and as a person, and what you still remember a year from now. This is a challenging course, and it is a lot of work. But many students have told me that it is very rewarding. There are many deliverables and assessments – that’s good: a bad day won’t undo your efforts for a whole term. And there are many opportunities for formative feedback to help you craft outstanding work.

I never “bell” grades. Your grades are independent of others’. That’s important: if you help others to learn, you will not jeopardize your own marks by raising the course average. I explicitly encourage collaboration, that helps everyone. But – remember the rules of attribution and academic integrity. Though you can be inspired by many sources, your work must be your own.

Components

In principle, the goal of the course is for you to deliver work for three key Integrator Units; you can also get credit for your lab journal, and participation and some other things. All of this can be completed in any sequence that makes sense to you, at any time, until the deadline to submit material.5 The deliverables usually contain a variety of options, one of the Integrator Units will be the basis for an Oral Test! The learning map contains four Integrator Units and you can choose any three of them and submit them for marking.

MGY441 2022 Marking Scheme

Activity Number Weight (each) Weight (total)
Two Integrator Units 2 18 36
One Integrator Unit for Oral Test 1 36 36
Your Course Journal 1 14 14
Participation 3 3 9
Your insights! page 1 5 5
Total 100

Grading Details

Go to …

  Oral Test Live Participants Participation Journal insights!  

Integrator Units

Integrator Units contain scenarios that integrate various aspects of the course; usually there is some story involved that provides context for the question you are pursuing. The goal is to assess your knowledge along a cross-section of skills: formulating a scientific question, preparing data, performing an analysis and interpreting the result. There may be several options for submission. You need to submit three Integrator Units out of four, but only two of those are normal submissions: one is the topic of your Oral Test. In order to do well, you should take advantage of formative feedback in regular “Learning Units” prior to your submission.`

Learning Units

Many Learning Units have components that work like small-scale integrator units, which you can submit for formative feedback. These units have a thick black outline on the Learning Unit map. Formative feedback means your submissions are graded with the same marking rubrics as your for-credit submission, and they are commented on, but the marks are not entered into the gradebook, they are meant to help you improve. Having received such feedback in at least one unit before each Integrator Unit submission is required.

Oral Test

Everybody goes into the Oral Test with anxiety, everybody comes out of it thinking it was not that bad at all. It’s a perfect way to assess your actual progress and if I had the bandwidth, I would make all assessments oral tests. You get immediate feedback, we can backtrack from mistakes, and if there are any errors of understanding, we can address them on the spot. Needless to say, it would be silly to focus on memorization-type tasks in such a test, rather, we will work along the “higher” levels of Bloom’s Taxonomy,6 and tasks could include things like reasoning about the quality of solutions, creating something new, organizing concepts, adapting material for new tasks etc. It’s meant to be challenging – but in a good way – assessment is not the same as judgment. Organizational details will be posted on Quercus; in principle you need to have material for an Integrator Unit prepared for your Oral Test and – although the test is cumulative – we will focus primarily on that unit. In all likelihood you will write a few lines of code. Make sure you have had enough practice.

Live Participants!

To improve engagement in our online lectures we will have four people on video in each class: myself, and three students. As we discuss topics that are relevant to the course our Live Participants will answer questions, search for answers and collaborate to explore solutions. In a sense this will be like an oral test, but not targeted to a specific learning unit. Your participation will be graded, and you can get major course credit for this, as follows:

…an alternative to the Oral Test

Grading Live Participants

How will the grading work? I am looking for engagement and interest, curiosity and creativity, the stamina to work through problems for the entire session, and knowledge and skills that are approximately in line with the progress of the course at that time. But this is not a test: it’s a team-learning experience and the learning is weighted more than the knowing. Somebody who asks all the good questions will do just as well as somebody who knows the answers.

 

Course Journal

Computational research employs the same best-practice principles as any wet-lab experiment. We ensure our work is reproducible, we take great care that our conclusions are supported by data, and we keep notes to document our objectives, activities and how we arrived at our results. Those notes are more than just a handy collection of information: they need to become a robust, testable record of activities. To practice this and form a habit of record-keeping, all students will keep a course journal as a Google doc, continuously throughout the course, and it will be marked at the end of the term.

Participation

I may not be the best source of explanations and your peers may explain things much more accessibly, and have a better idea where the sources of errors and misunderstanding really lie. Your contributions to discussions on the Quercus discussion forum, on technical issues and other topics will be evaluated as a participation mark. Details TBD – but I expect we will work on these things in part during the “tutorial” sessions. Your participations will be evaluated after the last day of September, October and November, i.e. in three portions. Helping others, and thinking up good questions about the material you have worked on is a great way to learn.

insights!

It is so very valuable to step back from time to time and ask yourself: what was really important about what I just did? What is the one thing I should remember? Maintaining such a high-level perspective goes a long way to ensure that your learning effort turns into something valuable. Begin an insights! document in your Google drive course folder that collects your most important ideas about this term. Focus on the essence of your experience. And if you can put it into rhyme – it will be all the more memorable.

Final Exam

This course does not have a final exam. You can focus on your other courses in the exam period. Or just relax.

Grading Principles

Marking Rubrics

I have written an extensive page on the criteria I apply for marking and I suggest you read that page carefully. It will not only help you for this course, but you can apply it to assessments in general.

How to do well

The one secret to do well in this course is continuous engagement. The continuous part is important since a lot of the course has to do with practical skills, especially with programming. This requires a very structured approach – a particular way of thinking actually – which one needs to get used to. That won’t happen immediately, but you will make very good progress if you work with the material just for a bit every day. The engagement part makes sure you don’t work mechanically. You take an active role, and you are mindful what the material means for you. You comment, you ask questions, you get in touch with me in case you feel what you are doing is pointless, or no fun. That’s how you learn.

Excellent and Outstanding

To excel at something means to surpass expectations. In general, if you complete a task to all of its specifications, that’s excellent, and I will be glad to give you up to 90% of the available marks (A). But outstanding is in a different league. An outstanding achievement (A+) advances the field, it extends what has been discussed, it makes an original contribution, it improves on previous ideas, it is elegant, and it is inspiring. Outstanding contributions make the world a better place, and striving for outstanding work makes you a better person. Giving you the tools for outstanding work is the goal of this course.

Online classes

Teaching and learning bioinformatics in an online format opens many opportunities. To realize them fully, we will build on the strengths of this mode of learning, such as its flexibility and the integration of rich media, and we will creatively manage potential problems, such as reduced opportunities for informal interactions.

A Change of Culture

We began University-wide online teaching in 2020 to protect students and educators from an extraordinarily contagious, novel Coronavirus that causes serious disease with not-yet adequately understood short- and long-term consequences to health. However, this does not mean that we must immediately resume physical contact once infection levels and manifest disease are significantly reduced in the vaccinated population. The benefits of online teaching7 (and, incidentally work-from-home in general) are many, and we can expect the quality to increase further as we grow experience. Yet we must remain aware of the downsides and address them through strategies that are fine-grained, detailed, specific, and personal. This is a fascinating challenge for our course.

In Practice

We can address some concerns right from the beginning: (I) Networking with students in the same Program or with similar interests can be initiated, we will discuss how. Contact can easily be established on Quercus. (II) To facilitate informal interactions between groups of students the University organises “Recognized Study Groups” – see below. (III) The Quercus discussion forum allows to have an ongoing discussion about engagement levels, general course satisfaction, and to address issues as the arise.

Recognized Study Groups

RSGs are groups of up to eight classmates in a course, who schedule regular online meetings. As per the Faculty:

An RSG for a particular course is created by a student who volunteers to be an RSG Leader. The RSG Leader is trained and chooses the day and time for their RSG to meet. Once the RSG is created, it is opened for classmates to join. An RSG Leader is not a tutor – they learn alongside the group. All group members participate in the RSG by reviewing course material, asking questions and preparing for tests together. In addition to your study group meetings, you will also get support from Study Group Assistants who help with study strategies and answering your questions.

These groups are created by one student who volunteers to become a RSG group leader and attends a training session. Students apply for this role and applications are now open. This sounds like an interesting development, and to learn more and/or start a group, visit the RSG Site at Sidney Smith Commons.

Organizational Details

Your technical setup needs to be adequate for the course – but there are other important considerations as well, including: time-management and study habits (continuous), our policies for assignment extensions (don’t), office hours (any time), and how we will run this course as a “safe space” and what this means for all of us (respect and kindness) and in particular regarding the privacy of recordings (what happens in the course stays in the course).

Technical requirements

The Office of the Vice Provost, Students has published a page on recommended Technology Requirements. This is useful, do visit that page, but what we need in this course may go a bit beyond this. Here is a list. If you can’t match these requirements, you need to upgrade before the course starts.

The systems requirements for this course are determined by the need to program in R/RStudio, run a modern Web browser, run the molecular visualization program Chimera X, and actively participate in multi-participant Zoom meetings.

Workload and time-management

The workload in this course is high, but you can make it play nice with your other courses because of our flexible schedule for deliverables. My estimate (using the Wakeforest University Courseload Estimator) comes to about 14 hours per week, based on ~50 pages of engaged reading, ~20 pages of research-level writing, 7 other assignments taken on average five hours each, and 2 hours of contact time. YMWV.

Time management

Time management is crucial in this course and you will need to start full-speed right away and not let up until you cross the finish line. Pause for a few days, break the habit, and it will be hard to get back to your best performance mode. The good news is, the finish line can be as close as you want: you may be done as early as October - that’s up to you, not me. Our due dates are quite open and give you a lot of flexibility if you keep one thing in mind: the due dates are the last dates on which assignments can be submitted. Never wait until the last date, you will run out of time to do other things. So get everything done as early as possible. The UofT Assignment Calculator looks helpful, although I think it could be nicely customized for this course.

Study habits

The single most important factor that determines how much you profit from a course is how actively you engage with it. This does not necessarily mean visible activity, but it means empathy: thinking along with the material and always striving to discover its meaning for you, yourself, your interests and likes and dislikes. One important way to promote this is to engage continuously, because it is frustrating to fall behind and this frustration will make it even harder to get back on track.10 And another aspect is keeping focussed: for example, taking notes during “lectures” is a great way to make sure you are actively listening.

Extensions for course work

Try not to require extensions. If you need an extension, this already means that planning has gone wrong. Just adding a few more days is not going to fix that – on the contrary, you may just be digging a deeper hole for yourself since this is probably not your only course. So if that happens, we should better jointly be talking to your registrar, whether you are getting all the learning help you need, and if there are perhaps some unresolved accessibility issues; perhaps we need a completely different study plan. We can work around a lot of issues to help you learn to your best capacity.

That said, here are the cornerstones of how this course interprets and implements Faculty policies: the key idea is that extensions must be fair, reasonable, and equitable.

Submissions due before the drop date (Wednesday, November 16 2022):
No extensions will be considered for these submissions.11 Such an extension would not be “fair, equitable and reasonable”, i.e. granting this to individual students would violate the requirement to give all students equal opportunity to succeed in the course. In fact, if you find yourself so far behind in the course that you are unable to submit meaningful work for assessment by that date, I highly recommend that you drop the course – you will not be able to complete the rest in time either.
Signing up for the Oral Tests:
The dates for the Oral Tests will most likely be bunched into the end of November, due to the ridiculously late 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 before the last day of class (Tuesday, December 6 2022 23:59):
Since the course does not have a final exam, the Faculty requires grades to be marked, collated and submitted a few days after the last day to submit course work in the Fall term. Thus the final deadline for all course work is Tuesday, December 7 2022, 23:59 EST. Given the grading requirement, I cannot normally grant extensions beyond this date. The Faculty allows so called informal extensions to be granted “in extraordinary circumstances”; in those cases too, the requirement to be “fair, equitable and reasonable” will apply, i.e. you would need to demonstrate that the need for the extension was due to unavoidable circumstances that go significantly beyond what was expected of the rest of the class, and submit “official” documentation to me. If that happens, (i) we would determine an adjusted submission date, (ii) I will initially submit a mark of 0 for the missing submissions, and (iii) I will submit an amended mark, after that date, if appropriate. Note that the Faculty requires that such extensions don’t go beyond a few days after the end of the Final Examination Period. If you require an extension beyond that date you need to submit a formal petition through your College Registrar.

In summary, everything about extensions is quite onerous, and it will be much better to work towards finishing your coursework far ahead of time – and you can!

“Office” hours and contact

You can get one-on-one feedback from your instructor or your TA. That said, there are no fixed office hours, I prefer to flexibly respond to your needs. Setting up a meeting will be a two-step process. We will email first, and you will find that discussions by e-mail are both more efficient and effective than meetings: you gedt tostructure your questions clearly, you have a document trail of what was discussed and can review it, I have a chance to find high-quality solutions, email can contain links to information sources, and we can share points of general interest more easily on the discussion forum. But if you do need to talk in person, we’ll find time to do so.

To contact us, we prefer that you use your utoronto.ca account; if you use another email account, be sure to identify yourself by name. Have a look at the Netiquette and Asking Technical Questions units before you do so.

No phone. No texts.

Prerequisites

Introductory courses to biochemistry and molecular biology provide some of the background material for the course. That might include the courses that are listed as prerequisites in the Calendar: BCH210H1/ BCH242Y1; BCH311H1/ MGY311Y1/ PSL350H1.12 However I have no way to assess how successful you were in these courses, nor do I know what material actually was covered, and thus I generally waive prerequisites – do let me know if you need a prerequisite waiver. Your level of preparation is your own, adult, responsibility; my responsibility is to make the course expectations as explicit as possible, and if you feel you can manage the material, go for it.

A breakdown of knowledge that I expect you to bring into the course is listed here.

This Course is a “Safe Space”

This course will do everything to ensure that all are welcome,13 and protected from harassment, judgmental behaviour, and harm. As a professional learning environment, the goal of this course is to foster and encourage engagement and creativity, to acknowledge strengths, to be helpful with weaknesses, to establish an enjoyable community on a basis of mutual trust, and to nurture personal growth. These are not empty words, they mean something to me and I trust that we are all in complete agreement.

I often see that students are embarrassed to speak up in class, are hesitant to discuss mistakes, feel that they would prefer to ask questions anonymously, etc. Please realize that these are already signs of a toxic environment that needs to be addressed, and they diminish what you could get out of a course. Your questions, whatever they are, are not only valid, they are valuable.

I wish that this characterizes how we will come together and conduct this term – however, the outside world may be different and thus I do not permit sharing of discussions, contributions, conversations etc. outside of class. This applies in particular to social media, including reddit, facebook, whatsapp, tiktok, discord etc. etc.

Sharing information about the course, its participants, and/or contents with others, in a way that discloses identifying information, or links material or events to specific individuals will constitute a breach of our “Safe Space” policy.

This is a simple principle that I need everyone to respect: What happens in the course stays in the course! Actually this merely implements in a specific way what the Student Code of Conduct requires of us all anyway. If you have any doubts or questions about this, please don’t make assumptions but contact me for clarification.

Names

I will use the first and last name that I find in my class roster, unless you request me to use a different name. You can change your “display first name” for UofT online services here. In Zoom meetings, I have to be able to identify your as a student in the course, and I will remove without warning14 any participant who I do not recognize as a student of the course. You can set your name in your Zoom user profile, or change it even after you have joined a meeting, from the “participants” list. If you have a Chinese name, please add the 汉字 on your _About me…” page in your Google docs folder – I can’t distinguish 怡 from 毅 from the English alone and would like to pronounce it correctly.

Land

It has become customary in academia to acknowledge the original owners of the land we live and work:

I wish to acknowledge this land on which the University of Toronto operates. For thousands of years it has been the traditional land of the Huron-Wendat, the Seneca, and the Mississaugas of the Credit. Today, this meeting place is still the home to many Indigenous people from across Turtle Island and we are grateful to have the opportunity to work on this land.

The above can be found on the site of our Indigenous Initiatives and land acknowledgement is considered a “protocol”. Though, I do have mixed feelings when I encounter this formula – (i) it seems too smooth, and too ritualistic to address the complex history of colonialization and genocide in Canada in a meaningful way; (ii) it does not really do, to profess a protocol without an understanding what your role is in this protocol, at this time, on this occasion; and (iii), such an acknowledgement can only be a small part of a relationship, a beginning.15 Thus I hope you can take this as an opportunity to add meaning to the protocol, understand what the words mean, reflect on the history of land ownership – specifically, our campus is part of the “Toronto Purchase” – learn more about the actual Treaty boundaries, here and elsewhere; and figure what out is meant by “Turtle Island”.16 This all is a part of engaging with the world around us with respect, which in turn is the key to grow, in and through the encounter.

Recordings

No Lecture Recordings, but …

Even though I do not plan to create shareable video recordings of lectures and the like, exceptions may arise and thus the following disclaimer applies and is assumed to be agreed on by you through your participation in the course.17 Two considerations guide us in principle: copyright considerations and privacy considerations.

According to the University’s Provostial Guidelines:

 

The unauthorised use of any form of device to audiotape, photograph, video-record or otherwise reproduce lectures, course notes or teaching materials provided by instructors is covered by the Canadian Copyright Act and is prohibited. Students must obtain prior written consent to such recording. In the case of private use by students with disabilities, the instructor’s consent must not be unreasonably withheld.

As the instructor, I may at times record this course, including your participation, and such recordings may be made available to students who are registered in the course, for viewing or listening remotely. As the Provost emphasizes, course videos and materials belong to the author of the recording and are protected by Canadian copyright law. You are not permitted to download, copy, or share any course or student materials, including but not limited to audio, video, images, or text - without the explicit permission of the copyright holder. In any case, any course-related material is for your personal use only. Any exceptions must be arranged in advance, with the consent of all involved parties.

Since this is a University Policy, Students who violate these terms will be subject to disciplinary actions under the Code of Student Conduct.18

Do contact me for any questions about recording and use of videos in which you appear, in particular in case you have significant reasons to opt out of recordings; in that case we will need to construct alternative arrangements specific to your circumstances.

Documentation of Assesments

I will generally record class-sessions and exams for documentation, since some of you receive marks at these occasions. Such recordings will not be shared, except as may be required by the University, for the purpose of administering the course. For example, we may need to review recordings to justify marks, or while resolving allegations of academic misconduct and the like. In that case, material will be strictly shared privately, on a need-to-know basis, and all recipients will be committed to the same terms.

Accessibility

This course is different in many ways from other courses you have taken or will take, and the accommodations that our accessibility counselors make may not actually work well since they don’t actually know the course. So, if you have any special needs,19 get in touch with me and we’ll work out the best way to support you. No big issues here, we do this every term.

Academic Integrity

This is the last item, but potentially the most consequential one. In order to work together in a mutual trust-based relation, this course takes academic integrity very serious. So serious in fact that it has its own learning unit. Academic integrity is often erronously condensed to concerns about cheating and plagiarism, but it is in fact a question of personal growth.

Such growth is the actual goal of the course. Bioinformatics is the path.

Resources

References

Armstrong, Patricia. 2010. “Bloom’s Taxonomy.” Vanderbilt University. Vanderbilt University. https://cft.vanderbilt.edu/guides-sub-pages/blooms-taxonomy/.
Prat, Chantel S, Tara M Madhyastha, Malayka J Mottarella, and Chu-Hsuan Kuo. 2020. “Relating Natural Language Aptitude to Individual Differences in Learning Programming Languages.” Scientific Reports 10 (1): 3817. https://doi.org/10.1038/s41598-020-60661-8.
Roth, Michael S. 2019. “Don’t Dismiss ‘Safe Spaces’.” The New York Times, August. https://www.nytimes.com/2019/08/29/opinion/safe-spaces-campus.html.
Toronto Governing Council, University of. 2019. “Code of Student Conduct.” University of Toronto Governing Council. https://governingcouncil.utoronto.ca/system/files/2020-03/Code of Student Conduct Dec 13 2019.pdf.
Toronto Vice-Provost Students, University of. 2016. “The Student’s Companion to the Code of Student Conduct.” University of Toronto, Office of the Vice-Provost, Students. http://www.viceprovoststudents.utoronto.ca/wp-content/uploads/The-Students-Companion-to-the-Student-Code-of-Conduct.pdf.
Wikipedia. 2021. “Bloom’s Taxonomy.” Wikipedia, The Free Encyclopedia. http://en.wikipedia.org/w/index.php?title=Bloom%27s%20taxonomy.

Page ID: MGY441-Syllabus

Keywords: Syllabus; Marking scheme; Procedural details

Author:
Boris Steipe ( <boris.steipe@utoronto.ca> )
Created:
2022-09-09
Last modified:
2022-10-04
Version:
2022.1.2
Version History:
–  (2022): 1.2 updated marking rubrics page
–  (2022): 1.1 added suggested timeline to learning map
–  (2022): 1.0 agreed with co-lecturers, submitted, and published
–  (2022): 0.2 first revisions: using Google Drive, clarifying formative feedback
–  (2022): 0.1 Import from BCH441 syllabus 2021 V 1.3 and update
To Do:
–  Collaboratively review
Tagged with:
–  Course Material
–  Live
–  Links to Map

 

[END]

  1. I call this a “lab” journal, because it is meant to be kept to the standards of recording lab-work, even though the work you do is not actually in a laboratory.↩︎

  2. If there is a delay with your enrollment, or you end up on a waiting list and can’t access the course page on Quercus, contact me so I can email you the information.↩︎

  3. … according to the industry-standard Tiobe Language Index↩︎

  4. Some people think of R as a kind of meta-language, a language that makes it easy to write “Domain-specific Languages”; that’s actually not a bad characterization – as long as you remember that in order to do that, all General Purpose Language requirements have to be satisfied as well. R is certainly not only used for statistics.↩︎

  5. You can find the detailed due dates on the course Assignments page on Quercus. Talk to me if the schedule does not fit your needs.↩︎

  6. Bloom’s Taxonomy is a very influential set of learning objectives in the cognitive-, affective-, and psychomotor domain that is used by many educators to scaffold their course creation. For example, in the cognitive domain, knowledge forms the basis of a hierarchy, whereas comprehension, application, _ evaluation, and creation form successively “higher” levels of achievement and more “valuable” goals (see also (Armstrong 2010; Wikipedia 2021)).↩︎

  7. Including: it is potentially more interactive; it is better suited to engage the whole class; it is easier to schedule guest contributions; commuting expenses are significantly reduced; commuting time is freed up; less barriers to attendance; meals can be prepared more economically at home; easier to organize child-care; more opportunities to integrate rich media and online resources; a general move from effort-based to results-based definition of work improves outcomes; the burden on environment and infrastructure is reduced; …↩︎

  8. Mac OS X is the preferred operating system in Bioinformatics since it runs Unix under the hood↩︎

  9. Here is a speed-test server.↩︎

  10. Duolingo works very hard to keep up such continuous engagement: “You’re on fire; keep up your 20 day streak and don’t lose it. How about doing a lesson right now?” … and they know exactly why.↩︎

  11. Since these requirements are so minimal, exceptions due to personal, medical, or accessibility reasons would require you to demonstrate (and document) that you have not been able to pursue academic work for that amount of time that you would normally have needed to fulfil the requirements. Given the volume of material, I would consider this time to be at least four weeks.↩︎

  12. Please check the official Calendar Entry for the official prerequisites↩︎

  13. I use the term “safe space” in a broad sense that is equitable, and inclusive of all. Much of our social discourse is structured along fault lines and leads to in-groups, wedge-issues, echo-chambers and the like. Such distinctions will have no meaning in this course. If the idea of a safe space seems to require more clarification, a recent NYT opEd by the president of Wesleyan University may be a workable introduction (Roth 2019), and we can certainly discuss this more.↩︎

  14. In meetings, I won’t have the time to ask who you are.↩︎

  15. For example, though I realize that in 2010 our territory was the subject of Canada’s largest land-claim settlement to that date, I can’t recall having had even one indigenous student in any class I have taught here. Given that some 2% of Toronto residents are first nations, if all else were equal, I would expect one in every class instead.↩︎

  16. Even more information can be found on this UofT Library Research Guide.↩︎

  17. This condenses and implements Faculty guidelines.↩︎

  18. cf. (Toronto Governing Council 2019; Toronto Vice-Provost Students 2016).↩︎

  19. I would be particularly interested if you are dyslexic, or have variant vision, whether we can adapt the layout of materials to your needs.↩︎