Posted by: idm04 | 2014/05/12

Fifth-year courses in UBC Sciences!

Courses listed here were taken between September 2013 and April 2014. The more I think about it, the sillier my naming system for these posts seems…

Other posts of potential interest:

First-year Courses in UBC Sciences!
Second-year Courses in UBC Sciences!
Third-year Courses in UBC Sciences!
Fourth-year Courses in UBC Sciences!

List of all courses I’ve taken

Courses in this post:
MICB 405
MICB 421
PHIL 330A

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MICB 405

I took this class because I needed another upper-level MICB course to graduate and I thought I’d learn something interesting/different than in typical MICB courses.

Grading Scheme

Research project 15%
Midterm 35%
Final 50%

We had the option of not writing the midterm, and having our final count for 85% of the final grade. Interestingly, nothing was mentioned about what would happen to the grading scheme if you were to write the midterm, but perform better on the final.

Material

The course covers a variety of topics in bioinformatics at an introductory level:

-Sequence databases, DNA sequencing
-Sequence alignment & assembly
-Phylogenetic trees
-Genome browsing
-Genomics in public health
-Functional genomics, transcriptomics
-Protein families and function, protein structure, proteomics
-Metagenomics
-Epigenomics

There was no textbook for the course.

In-class activity

For the most part, ‘regular’ lectures were given with the Powerpoint shown on the screen. Sometimes there would be demonstrations of tools (e.g. using BLAST) in class. There were some activities that lasted the whole class (e.g. de novo genome assembly by hand orz), and the occasional handout for some bonus points!

There was a weekly tutorial in which the TA went over some of the class material that week, or we would do some sort of learning activity like using BLAST.

Workload/Project

The workload for the course is light — there aren’t any regular assignments or readings; just the project and exams.

For the project, you’re basically given a dataset (everyone is given the same dataset) and asked to perform some sort of bioinformatic analyses on it (up to you what you want to look at). This was a group project (groups of 4 people) and we were able to choose our group members. We were given the genomic sequence data of two newly sequenced Bordetella strains, and our group decided to look at a particular virulence factor in Bordetella pertussis and see if we could find homologs in the other two strains, which are non-pathogenic. Since there’s no rubric for the project, I recommend starting early and meeting regularly with the instructor/TA to make sure you’re on the right track and get feedback.

Preparation/grades

The average in 2013W for this course was 80%, and I managed to get an A-.

I did not do as well as I thought I would on the midterm. I based my studying for the midterm solely on the “learning outcomes” which were given at the beginning of class, and skimmed over everything else. There were also questions I got wrong because of keywords that I had missing. For example, I had marks taken off for using ‘contiguous sequences’ instead of ‘contig’.

My advice would basically be to understand and remember everything, but focus on what is emphasized in class (don’t use the learning outcomes to narrow your studying). Taking good notes is also recommended because many slides are just pictures that don’t have an accompanying caption explaining it. Also, try to use ‘keywords’ to answer the questions on the exam.

In terms of practice questions, no practice midterm was given out, but the questions at the end of each lecture were meant to be examples of possible exam questions. The final was similar in style to the midterm, with heavy focus on post-midterm material.

Overall impressions

This course was interesting to me in the sense that it was much different than the more traditional MICB courses, and introduced me to the computational tools used in biological research. The course covered a broad spectrum of topics in bioinformatics and as such, I felt that sometimes we skimmed the surface and didn’t really go into detail enough for us to be able to use the tool. Other times, the details about some computational tools were confusing given our lack of knowledge about bioinformatics, and at these times I felt there wasn’t enough background info. I also felt unsure about what we actually needed to know for the exams and what was just extra info.

I did however, learn how to use some basic tools (the different variants of BLAST, MUSCLE for multiple sequence alignment, etc). Overall, I think the course is good for those interested in getting an overview of what bioinformatics tools are used for in research.

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In progress, to be updated by July.

MICB 421/447 is a research project based experimental microbiology course. The project lasts most of the term and is done in groups of 4 (sometimes 3).

You can take MICB 421 or 447 to graduate in the MBIM program. From what I heard, there was no midterm nor final nor “first lab” in 447, whereas there was a (optional) MT and mandatory final in 421, plus a lab (project 1 — it was on RNA accumulation in E. coli). I have no recommendations about which course to take — there are advantages and disadvantages of not having a final. Most people choose between 421 and 447 based on (1) their course schedule, and (2) what their friends are taking.

If you know the group of 4 (includes yourself, so 3 others) that you want to work with, register in the same section (e.g. Tues or Wed or Thurs). Choose your teammates wisely — choose people you’d work well with, and not necessarily people you’re friends with. Note that teams of friends in 447/421 are no longer friends by the end of the course. (I’m kidding…. kind of….)

MICB 421

Grading Scheme

Material

In-class activity

Workload

Assignments
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PHIL 330A

Took this class in political philosophy because I needed another upper-level course and it sounded cool.

Grading Scheme

Clicker questions – 10% (half participation, half correctness)
3 short papers – 10% each
Final paper – 30%
Exam – 30%

Material

The following topics were covered:

Utilitarianism (2 classes)
Rawls (10 classes)
Liberal egalitarianism ie. Dworkin/Cohen/Anderson (5 classes)
Libertarianism (4 classes)
Marxism (2 classes)
Communitarianism (2 classes)

In-class activity

The day would usually start off with a quick clicker question or two at the very beginning of class, probably meant to encourage arrival on time and therefore, attendance. The clicker question was usually based off the readings and if you read them, you’d get the question right.

For the rest of the class, we went through the slides with plenty of discussion.

Unfortunately, the slides weren’t posted in advance and I found it quite difficult to copy down notes while listening to the prof.

Papers

There were five opportunities to write a short (2-3 page double spaced) paper throughout the course, and out of those 5, we were to pick 3 to write on, worth 10% each. The paper topics were given the week before the due date, and sometimes there were more than one question to choose from. There was an opportunity to write a short paper every 2 weeks ish.

The final paper, worth 30%, was 6-8 pages long, double spaced, and could have either been an expansion of one of the 3 short papers already written or a brand new one on any of the potential paper topics. I think formulating your own paper topic was possible with permission.

I got plenty of constructive feedback on my papers, which was useful, and my mark for the my 3rd paper was significantly higher than my 1st.

Textbook/Readings

The main source of readings came from Kymlicka’s Contemporary Political Philosophy: An Introduction (2nd ed, with the grey cover) which I generally liked reading. I bought a used copy from Amazon.com for $25.30 before tax/S&H, but had to pick it up from my US mailbox.

For the section on Rawls, we were expected to read Rawls’ Theory of Justice (Revised ed). I borrowed it from my friend who had used it for PHIL 230A. We only read 2 chapters of the book…

We also did readings on other people like Cohen/Dworkin/Anderson but those were supplied through Connect.

Workload/Difficulty

The short papers took me on average about 10 hours total from start to finish, although you could probably write one faster than me if you have better notes (my notes weren’t that great…)

The readings took quite a while (40-60 pages on average per week, ~5 hours of readings per week), especially for the section on Rawls — I highly dislike reading his book. The Kymlicka readings seemed difficult to understand at first but I got used to it pretty quickly and it helped going through the more ‘difficult’ sections more than once.

The material is kind of difficult — the prof said we might want to reconsider taking the course if we hadn’t taken PHIL 230A, and near the beginning of the course (the beginning of Rawls), I felt a little overwhelmed by the material because some parts were difficult to understand. However, I chose to stick with the course and it turned out fine. The PHIL courses I took before this course were PHIL 220A and PHIL 433A, which honestly didn’t seem to help too much anyway, except maybe 433A helped with essay writing and for introductions to Kant, Rawls, and utilitarianism in the context of ethics.

Grades/preparation

The average was 68% and I managed to get an A-.

As with any course that involves reading works and writing essays, I highly recommend using sticky notes while you’re reading so you can easily reference or make notes on important sections or sections you want to re-read so that’s it’s easier to find them when you write your essays.

Reviewing your notes regularly helps a lot for the essays because then you don’t need to go re-read the textbook when it’s time to write the essay like I did…

We were given a list of potential exam questions a few (4?) days before the final exam. The questions involved a combination of at least two of the topics, for example Rawls and libertarianism, or perhaps Rawls and communitarianism, etc. I would expect to be tested on two of any of the topics except utilitarianism and Marxism. I didn’t start studying until we received the potential exam questions, but I could have started reviewing Rawls/libertarianism/liberalism/communitarianism.

Overall impressions

Interesting (and somewhat challenging) course and a refreshing break from Sciences.

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DO YOUR GRAD CHECKS IF YOU WANT TO GRAD. Will update later

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Responses

  1. Which would be a better choice: MICB 421 or MICB 447?

    • In 2013W, 447 seemed to be better — no exams, no Experiment 1*, you could work in teams of two or on your own. In 421, there was a midterm (optional), final, an Experiment 1*, and you could only work in teams of four (or three under some circumstances).

      However, I have heard some of these details may have already changed, so I really don’t know how if these details hold. Ultimately, I’d go with whichever fits better in your schedule. Looking at the SSC Course Schedule (which may not be finalized), 447 does have only a 8 AM Tuesday class, whereas 421 has the 8 AM class on both Tues and Thurs.

      * Experiment 1 was a ‘regular’ or guided lab like in previous lab courses where you’re given a question to investigate as well as the general procedures for the experiment.

      • Thank you for your feedback!

        I’m not planning to skip class or anything, but would you think that the lectures (scheduled at 8am) are mandatory to attend in order to get a decent mark? I live pretty far from UBC (more than one hour commute) so it would be difficult for me to go to school so early :(

        • Sorry for the delay, I didn’t have internet for a few days.

          They do give you important info about lab procedures, but it is not necessary to attend to do well. I believe the instructors do keep track of the attendance to some extent. If you do miss class, just check with your teammates.


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