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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 syllabus for CSB195 - Computational Biology Foundations, created and first taught in 2022. I’m very excited about this new course, which I envision as an introduction to “computational thinking” in biology, and elsewhere.

See you “in class” !

 

The Course

Our understanding of life is built from observation, abstraction, modeling, and comparison. In this First Year Foundations course we explore how these activities are based on concepts of chance and choice, of organization and dispersion, of cooperation and conflict, and how these ideas inform domains such as statistics, computer science, bioinformatics, molecular biology, physiology and ecology. Through this, we build a broad framework of relationships and connections that will make your engagement with specialized courses throughout the sciences all the more meaningful. This course’s focus on best practices of structuring project work, using tools and resources, and documentation, will be valuable preparation for all subsequent courses.

The course topics

CSB195 is conceived to explore the foundfations of computational biology, the idea that biologicval insights can be obtained from the use of computational tools. As this is a new course, the exact contents we will cover are still somewhat fluid, but they will likely include concpets of information, random fluctations and the resulting distribution of states, probability and significance, as well as the concepts and databases we use to store information about biological sequences, structures and functions. An important part of the course will be to write computer code to explore our concepts.

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 form a general map of relationships, through which you can organize knowledge in your future studies; you will improve your general computer literacy, and you will learn to read and write computer code, primarily in the programming language R. Writing your own code has become indispensable in any life-science laboratory, so, yes, you will start to write your own code.

Instructor

Boris Steipe (<boris.steipe@utoronto.ca>)

Locations

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

  1. Some learning material is in HTML pages on this server.
  2. Programming tasks start from a RStudio project that lives on GitHub: the “basic setup” project, as a first introduction. All programing will be done on your own computer and all the tools you work with can become part of your future work in other courses.
  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. For details, see the
  4. The course page on Quercus is our hub for course-administration mechanics; we will also make good use of the Discussion Board.
  5. Zoom will provide our primary classroom. Each week’s URL for our Zoom meetings will be announced via Quercus, a few minutes before the meeting begins.
  6. Finally, our tutorial sessions will probably be in-person, in the Anthropology 120 classroom. I say probably, because I don’t know yet whether the room is suitable, and a resurgence of COVID may make such meetings unadvisable. Please note that I require all occupants of the classroom to wear well fitting medical masks that fully cover nose and mouth at all times - maitaining productive social interactions while being properly protected is a learning objective of this course and accordingly you will lose course marks for non-compliance.

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 Monday, September 12. 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 Mondays from 13:10 to 15:00 (for two hours of class online), and Wednesdays from 17:10 to 18:00 (for one hour of in-person tutorial). Do keep your calendar open for the entire time, there will be no lecture recordings: you actually need to be there, at the time, to participate; your attendance is necessary.

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

CSB195 is primarily taught in an online classroom, and learned from exploring various tasks on your own. Marked assessments include submitted reports; an Oral Test; keeping a Course Journal; participation in asking and answering questions; and recording some meaningful insights on your learning progress.

Why apply computation to biology? Why use “R”?

Learning to Program

Why program in the first place? There are two reasons. One is: writing code 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 languages3. 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 - though I hope to make some use of both languages over the term;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 …

This course is conceived to be suitable for absolute newcomers. If you find that you are having an unreasonably hard time with reading and writing code, contact me as early as possible so we can get you the help you need. 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. Research has shown that it an aptitude to learning natural languages is actually more important than “numeracy” in this regard (Prat et al. 2020). If you’re looking forward to work hard on something new and valuable, then I am confident you will do well.

Getting started: the map

The key entry point for the course is the Learning Map. This map is a subset from my fourth-year bioinformatics course and it contains integrated, standalone resources.

The Learning Map is the entry point into learning course-related skills. Click to load. Then bookmark, scale and study.

The Learning Map is the entry point into learning course-related skills. Click to load. Then bookmark, scale and study.

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

Learning Units with a   black border   have deliverables that contribute to your coursemarks. 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. There are many deliverables and assessments – that’s good: a bad day won’t undo your efforts for a whole term.

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 reports; you can also get credit for your lab journal, and participation and some other things. You can find the detailed due dates on the course Assignments page on Quercus. 5

CSB195 2022 Marking Scheme

Activity Number Weight (each) Weight (total)
First report 1 15 15
Second report 1 20 20
Third report and Oral Test 1 30 30
Your Course Journal 1 15 15
Participation 3 5 15
Your insights! page 1 5 5
Total 100

Grading Details

Go to …

  Reports Oral Test Participation Journal insights!  

Reports

Reports will document your understanding of a particular topic. They will require writing text, crafting images and code, and proper referencing.`Refer to the General section of the marking rubrics page I use.

Oral Test

Your third report will be evaluated in an 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.

 

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. Thus I would like to build up resources of FAQs and self-evaluation questions over time. 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

One secret to do well in this course is continuous engagement. The continuous part is important since “a part of the course has to do with practical skills, especially with programming.”Computational thinking” is a habit, not a piece of knowledge and you need to get used to it. 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 probably high. My estimate (using the Wakeforest University Courseload Estimator) comes to about 15 hours per week, based on ~20 pages of engaged reading per week, ~40 pages of research-level writing per term, and 3 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. 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 (Monday, December 5 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 Monday, December 6 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

There are no fixed office hours, I prefer to flexibly respond to your needs. That said, setting up a meeting will be a two-step process. We will eMail first, and in my experience almost all issues can be resolved by email. You will find that discussions by e-mail are both more efficient and effective than meetings: 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 with the class. But if you do need to talk, we’ll find time to do so.

You can email me at <boris.steipe@utoronto.ca> at any time. I prefer that you use your mail.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.

This Course is a “Safe Space”

This course will do everything to ensure that all are welcome,12 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 warning13 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.14 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”.15 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.16 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.17

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,18 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. Computational biology is the path.

Resources

References

Armstrong, Patricia. 2010. “Blooms 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 Students 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. “Blooms Taxonomy.” Wikipedia, The Free Encyclopedia. http://en.wikipedia.org/w/index.php?title=Bloom%27s%20taxonomy.

Page ID: CSB195-Syllabus

Keywords: Syllabus; Marking scheme; Procedural details

Author:
Boris Steipe ( <boris.steipe@utoronto.ca> )
Created:
2022-09-11
Last modified:
2022-10-05
Version:
2022.1.1
Version History:
–  (2022): 1.1 updated marking rubrics page
–  (2022): 1.0 Revise to CSB195 specific contents
–  (2022): 0.1 Import from BCH441 syllabus 2021 V 1.3 and update
To Do:
–  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. Talk to me if the schedule does not fit yur 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. 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.↩︎

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

  14. 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.↩︎

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

  16. This condenses and implements Faculty guidelines.↩︎

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

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