Posted by: idm04 | 2015/06/27

Bachelor of Computer Science (BCS): Year 1 Term 2 Course Review

Courses I took this term:

CPSC 210
STAT 302
MEDG 421
MICB 425

List of all courses I’ve taken

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CPSC 210: Software Construction

One-line summary: This course was intense and immersive, but I’m glad I can say I now know some Java.

Grading scheme:

Updated information about the grading scheme is available on the CPSC 210 website. You can also read descriptions about each of these on the website.

Final Exam 40%
Labs 10%
Project 15%
Assignments 5%
Quiz 10%
Midterm 20%

Syllabus:

This list probably won’t make sense unless you’ve already learned some of these things on your own or at another school…

Basically, we learned Java and object oriented programming. A lot of the things we covered were abstract.

Control and Data Models
Data Abstraction
Type Hierarchy, Polymorphism, Dispatching
Robust Classes
Implementing an Object-Oriented (OO) Design
Extracting an OO Design
Design Principles (Coupling and Cohesion)
Observer Pattern
Composite Pattern (think trees)
Iteration Abstraction

In-class activities:

Lectures generally involved the instructor going over code, or drawing diagrams on the projector. Unlike 110, we did not work on problems by ourselves most of the time. However, every few lectures, there was something called a “lecture/lab” in which we were given a problem to work on on our laptops and ask for help if necessary. Unfortunately, we were usually only given ~15 minutes to work on it, which was not enough time to complete the lecture/lab in class.

I found it difficult to take notes in this class because copying code by hand is difficult, and because explanation of diagrams/code was usually verbal rather than written. Fortunately, there are videotaped lectures posted online from 2013W, which I found very helpful for reviewing.

Lab:

There were five labs to attend, once a week, during the first half of the term. It was not required to attend labs after that, aside from the project marking at the end of term. Each lab was due at the beginning of the next lab session. Labs were focused on practical aspects, like how to write tests for a Java program, and I found them much more interesting/engaging than lectures. We were allowed to leave the lab during the lab session after being marked, or if we weren’t being marked that lab.

Our lab mark was based on at least two randomly assigned labs (out of the five labs).

Assignments:

Like lab, we only had assignments for approximately the first half of the term. Assignments were generally straightforward. We had to hand in our code online for the assignments to be automatically graded by running the handed in code against a series of tests. We were immediately given the score and were allowed to change and re-submit our code as many times as we wanted before the deadline for the assignment.

Project:

The project started halfway through the term, after all the assignments and labs had finished.

Our project involved developing an Android app that would plot UBC student schedules on a map, and determine whether two students can meet at a given time (ie. if they have mutual breaks), and if so, where they could meet on campus. A lot of the “backbone” of the code was already given to us; we just had to add certain functionality.

The project was also broken down into two phases, and smaller, more manageable tasks for each phase. We were to work on the project on our own, although in previous versions of CPSC 210, the project was done in pairs. I found the project to be challenging, but very doable as long as I started early. The TAs and instructors were also available to answer questions on Piazza. I don’t think I would have completed the project without consulting Piazza.

Readings:

There was no textbook, but readings were assigned online. Many of the readings didn’t make sense to me until I re-read them for the second or third time, but re-reading them was an important part of my review for the exams.

I have heard complaints from other students about the readings being difficult to understand and abstract. It may be worthwhile to consult other resources, such as Big Java, or Java Software Solutions, or something else (there are many resources).

Tips:

Start the project early and work on it regularly. The project takes a lot of time, and it would generally be a terrible idea to start the same week that it’s due. Many students started very late and couldn’t get a score greater than zero from the automated grader by the deadline of the first phase of the project. Most people will need some help with the project, whether that be through TA/office hours or through Piazza. It may be increasingly difficult to get help closer to the deadline because others may also be in the same position as you. I also recommend handing in the project early, because the online repository to which you submit code is not completely reliable, and may have technical issues especially when everyone is trying to submit a few minutes before the deadline.

On that note, also make sure to commit your project to the online repository regularly so that you have your code backed up in case the program/computer crashes. One of my friends told me that his friend’s computer crashed while he was halfway through the first phase, resulting in all that work being lost (he hadn’t yet committed). I also overheard a student talking to an instructor about how his computer crashed the day before the project was due, resulting in all his work being lost (he hadn’t yet committed either).

We had to learn a lot of things on our own in this class, which was kind of intimidating, but it was intended and it was a good experience. When you’re working on a project, you have to be able to look up some things on your own. That being said, the TAs and instructors were very helpful and dedicated a lot of time and effort in guiding students to the right places/solutions throughout the project and the course.

I felt it was important to pay attention in class in order to be prepared for the exams, because lecture notes aren’t posted (at least, ones that make sense without much context) and the other materials (e.g. online readings) do not adequately cover the material on their own. One can also review the videotaped lectures from 2013W online, which is what I did for the final.

I suggest using some lab time during the first half of the course, to ask the TAs questions about any lecture material that may be confusing. During this time, TAs aren’t doing much in labs, because the labs are fairly straightforward and so people don’t need much help with them.

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STAT 302: Introduction to Probability

One-line summary: This was a fun course for me. Not sure when I’ll ever apply what I learned though. I took it in part so that I could take more stats, so we’ll see…

Note: Eugenia was the instructor for the offering of the course that I took. I looked on Piazza for the previous term’s offering and it seemed quite different, unexpectedly.

Grading scheme:

Written assignments (four total) 16%
WebWork online assignments (bi-weekly) 9%
Midterm 25%
Clicker 5%
Final (must pass to pass course) 45%

Syllabus:

1. Principles of counting: premutations and combinations
2. Definitions and rules of probability, conditional probability, conditional independence
3. Discrete and continuous probability distributions
– random variables, expected values, functions of random variables
4. Bivariate and multivariate probability distributions
– joint, marginal, and conditional distributions, conditional expectations, moment generating functions
5. Limit theorems
– convergence in probability, convergence in distribution, Central Limit Theorem

In-class activities:

I should mention that I was initially in MATH 302 so that I didn’t have to have a three hour break on Tues/Thurs, but after one class of MATH 302 I quickly left and joined STAT 302, which was taught by Eugenia.

We usually went over the lecture notes posted online, which consisted of reviewing theory as well as stepping through example problems. There were usually a few clicker questions each class. Every few classes we would also have worksheets that we worked on in assigned groups.

Solutions to example problems were not posted online, but were available at office hours.

Assignments:

There were four written assignments. Some questions were pretty easy, but some were quite difficult and took me a frustratingly long time to complete. I spent anywhere from four to over ten hours on each assignment. I recommend starting them early so that you can ask the TAs for help. The TA office hours were very helpful for assignments.

Webwork:

The Webwork online assignments were more straightforward than the written assignments and took far less time. We got several tries for most questions.

Readings/Textbook:

I don’t think there were assigned readings, but there was an assigned textbook and suggested practice problems from the textbook. I did not purchase the textbook, and I know many people found a copy online. I think the textbook would be useful if you wanted extra practice with the material, but most of the time the practice given is sufficient (in-class examples, assignments, webwork).

Tips:

As with most stat/math courses, practice is important to understanding the material and doing well. The midterm was only 60 minutes long but there were many questions and I did not have time to check it over. This means that reading over the notes is most likely insufficient to doing well. Practice is key.

Assignments can be more difficult than they look, so I recommend starting on them early so that you can get help early.

I found making a cheat sheet (which we were allowed to for the final) really helpful. Aside from that, I redid some of the Webwork questions, in-class examples, and a few of the assignment questions, to study for the exams.

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MEDG 421: Genetics and Cell Biology of Cancer

Short summary: I found this course quite interesting and I learned a lot about the paradigms of cancer cell biology, particularly about how cancer develops and evolves, current and past efforts to treat cancer, and why treating cancer remains so difficult. I found the grading/assessment in this course to be in some ways, unorthodox. If you are interested in cancer biology and do not mind putting in some work/effort for a grade in the 80s, I would recommend this course.

Note: When I took this course, it was full before the course started, but there were several seats remaining by the course drop date.

Prerequisites:

When I took the course, the prerequisites were BIOL 335 and one of BIOL 234, BIOL 362, BIOC 302, BIOC 303. However, I did not have BIOL 335. In my opinion, the knowledge I would have gained from taking BIOL 335 or BIOC 302 would not have been necessary for this course. The course coordinator did not seem strict about the prerequisites.

Grading scheme:

Article summaries 20%
Cancer e-book contributions 20%
Book club report/participation 20%
Midterm 20%
Final 20%

Each of the graded components were weighted equally, which I find strange. It seems rational to me that components would be weighted depending on the extent to which they test the student’s knowledge, and depending on the effort expected. As such, it was unusual that the midterm and final were only weighted 20%.

Syllabus (topics below are for each lecture):

1. Transformation
2. Oncogenes
3. Tumour suppressor genes
4. Protein tyrosine phosphatases
5. Genome stability
6. Autophagy
7. Stem cells
8. Immunity and cancer
9. Genetic testing with next generation sequencing (NGS)
10. Moving to treatments
11. Cancer genomics
12. Pediatric cancer genomics
13. Pharmacogenomics
14. Lymphoma
15. Genetic counselling & cancer genes
16. Angiogenesis
17. Cancer immunotherapy
18. Ovarian cancer
19. Cancer epigenetics
20. Retroviruses and cancer
21. Prostate cancer
22. Lung cancer

In-class activities:

For the most part, each lecture was given by a different speaker who was a researcher in some area of cancer biology. One of the reasons I found this course valuable was because I heard from a wide variety of cancer researchers on their area of expertise.

The lectures were usually traditional lecture format = slides + lecturing. Slides are posted online sometime after class.

Article Summaries:

We were required to summarize five research papers chosen from specific areas throughout the term. Only one student per paper was allowed, which was enforced by having us sign up the pubmed id online. Fortunately, I never had the issue of signing up for a paper that was already chosen, even when I signed up relatively late. It is feasible to sign up for the five papers all at once, and they can be changed.

It was recommended to choose papers that relate to a particular pathway or cancer, because it makes summarizing the later papers easier because you can use your previous background knowledge from the earlier papers. Choose review articles or letters (short versions of papers) was discouraged.

The time I spent summarizing each paper depended on how difficult I found it to read the paper, so choose wisely. I spent many hours for the first paper summary, and the time I spent slowly decreased as the term went on.

I found the marking of the paper summaries very strict and subjective, and towards the later paper summaries, not constructive. The highest mark I received was 18.5/20, and it seemed like marks were taken off our summaries just so that no one (or very, very few) got higher than 19/20. Following the rubric is really important to doing as well as possible on the paper summaries. Other than trying to understand the jargon in the papers, I also found it difficult to summarize papers in only one page with 1.5 spacing. You may have parts in your paper summary that seem important, but need to be omitted in order to meet the page limit. For example, a paper usually has several key findings and possibly a few minor related findings. In such cases, I sometimes presented one or two of the more important findings and omitted the other ones to meet the page limit.

I will post my article summaries if I remember (remind me if I don’t). Article summaries had to be submitted to turnitin.com.

Cancer e-book:

When I took the course, there was an e-book being developed for the course, and we were expected to contribute to it. Initially, we were required to submit a report on a specific topic as well as edit three reports from other people, but the editing part was removed. However, we still had to edit chapters of the e-book written in previous years, which consisted of adding new paragraphs, rewriting sentences, and inserting figures which could be original work or Creative Commons.

In my case, the report was on Nobel prize work that was relevant to cancer research and was 750 words in length. I received 14/15 on my first draft and chose not to revise. I’ll post it here if I remember.

As for editing the chapters, I mostly just made edits to grammar, formatting, and to the bibliography, which were relatively insignificant edits. However, I did save often, which probably resulted in there being many edits under my name. I received a mark of 7/10 for editing which I was pleased with, given my efforts.

The editing was worth 8 out of the 20% for the Cancer e-book mark, and the report was worth the remaining 12%.

For any reports where references are needed, I highly, highly recommend using a citation manager such as Zotero. I have used RefWorks before as it was recommended in MICB 421 and SCIE 300, but Zotero is far superior and is free for anyone to use. The integration with browsers including Chrome and Firefox, as well as integration with Microsoft Word is amazing and it is extremely convenient and easy to learn and use.

Book club report/participation:

We were required to choose one of three books to read and write a two page report on. I chose The Philadelphia Chromosome by Jessica Wapner, which I read over a couple days during Reading Break.

NOTE: I am selling The Philadelphia Chromosome for $20.

I’ll post my report here if I remember. I only received 85% or something like that which was disappointing because after the instructor talked about the book report, I was under the impression that it would be marked quite leniently, and no criteria were given. The only feedback I got on the report was a comment saying “Good job” so I’m not sure where I lost marks. As with the paper summaries, I felt that marks were taken off to control grades.

As with reading any book for any course, use sticky notes while reading to bookmark/highlight key passages. This makes it much easier to find them and refer to them when you are writing the report.

Aside from the summary, there was a group discussion of the book during one of the lectures.

Readings/Textbook:

No textbook was required for the course. If you want to read a textbook, the e-book is easy to read and gives a good intro to many topics in cancer biology.

Exams:

The exams are open book, and there are previous exams available online. Do have a look through them because the questions on past exams are a good representation of what to expect, and the questions seem somewhat unorthodox and easy to misinterpret. One of the things I really liked about this course was that problem solving was valued over memorization, which is untrue in many other courses I have taken.

For the open book exam, I printed out the notes for each lecture and stapled each lecture together so that I could go through my stack of labeled lectures easily and pick out the relevant lecture for the question.

It was important to answer the exam questions both clearly and with as much detail as possible. Despite the questions being open ended, there was usually only one or two ‘right’ answers that got full marks, and they were generally pretty obvious.

The average and median for the midterm was approximately 68%. The highest mark for the midterm was a mere 84%, and I managed to get 83%. The instructors said they did not expect the grades to be so low, and it seemed that many people were disappointed with their marks. A lot of people simply completely missed what the question was asking for on at least one question (and therefore failed that question), and there were only five questions on the exam. The instructors hinted at substantial scaling for the midterm.

In my opinion, people found the exam difficult because it is unlike other exams in life science courses. There were only five questions on the exam, and they were all open-ended, but the marking was strict. This generally makes for low marks.

Another reason why I think the grades were so low was because of unfair marking. Despite my relatively high mark of 83%, there was many examples in my midterm and undoubtedly in others’ midterms where marks were docked unfairly. One example — there was a question that asked us to describe and explain an event that could occur in a patient with melanoma that would result in failure of the combination therapy Raf inhibitor + MEK inhibitor.

My answer: “A mutation occurs in the gene coding for the MEK protein such that the MEK inhibitor no longer binds to the MEK protein. MEK can have its ‘normal’ downstream effects resulting in activation of pathways in cell division, survival, and migration.”

Answer key:
-mutation in gene for MEK protein so that inhibitor doesn’t bind
-MEK no longer inhibited, can activate pathways in cell division etc

Despite my answer being identical in content to the answer key, I was docked several marks. When I approached the TA about it, she took several minutes to look at it, and then decided to tell me that she was looking for more detail.

Another example — one question described a clinical scenario and asked us to give one hypothesis of what could be going on. In the answer key, TWO hypotheses were needed for full marks.

(Summary of) Tips:

1. When given, follow the rubric.

2. Use Zotero for references.

3. Use sticky notes while reading the book for the book report.

4. For exam questions, read the question carefully and find out exactly what it is asking so you can frame your answer properly. For example, if it asks to propose a hypothesis for a phenomena and propose an experiment to test it, then make sure you do exactly that in your answer. It would also make sense to explain how to interpret the results.

Furthermore, despite the question being open-ended, it is sometimes obvious what answer they want, and each question is usually related to a specific lecture. For example, one question described chromosomes of abnormal structure and number, and asked us to “suggest” two mechanisms that might lead to this phenomena. In class, we talked about several mechanisms that resulted in chromosomal abnormalities. All we needed to do was to describe two of them in our answer.

Based on past exam answer keys, you can to some extent predict what key words and what details they’ll be looking for in your answer. If in doubt, just write as much as possible, which increases the probability that you’ll have key words or explanations that match part of the answer key.

5. Don’t worry too much about grades. See below.

Grades/Workload:

I have probably made it seem like the marking style can be quite unfavourable in this course, which may discourage people from taking it. Whether I would recommend this course depends on your goals. The majority of people who take this class receive a grade in the 80s. If you are interested in cancer biology and do not mind putting in some work/effort for a grade in the 80s, I would recommend this course. If you intend to get a 90+ in this course, it will most likely be a lot of work, and in my opinion, not really worth it. If you wish to get as high a grade as possible in this course, you may not enjoy it. If you are interested in learning about cancer cell biology and genetics but don’t want to deal with doing paper summaries and writing a portion of someone’s textbook for free, you could consider just sitting in the lectures.

I did not find the workload to be that bad, but I also wasn’t trying very hard to get a high grade, especially after the midterm. I spent three hours a week on average on this course outside of lectures, spent a day studying for the final, and ended up with 83%, which I am quite satisfied with given my effort. The average for my year was 80%. The highest mark in my year was 93%.

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MICB 425: Microbial Ecological Genomics

One-line summary: One of my favourite MICB courses. A lot of emphasis on critical thinking. Small assignments, group discussions, and no exams.

Grading scheme:

Five “Evidence Worksheets” 25%
Five problem sets 25%
Four writing assignments 25%
Participation 25%

Syllabus:

Module 1 – Origins and earth systems
– How did life originate and evolve over geological timescales?
– What roles do microbes play in global geochemical cycles and how do they support other life forms?
– What is our current understanding of global microbial diversity and abundance and what gaps are there in our knowledge?
Module 2 – Remapping the body of the world
– What methods are used to study microbial community genomics and what limitations are there?
– What does the structure and metabolism of a microbial community look like, and how does it impact the Earth?
Module 3 – Agents of open source evolution, microbial species concepts
– How prevalent is horizontal gene transfer (HGT) and what role does it play in the evolution and diversity of microbes?
– What role does HGT play in the preservation of biogeochemical pathways?
– How diverse are microbial populations and microbial ‘species’?
– What are the models for microbial species concepts and what are their limitations?
Module 4 – Distributed metabolic networks/bioinformatics?
– Using MEGAN
– How does BLAST work?

In-class activities:

Class usually consisted of either short lectures by the instructor, group presentations from students, whole class discussions about the readings/material, or small group activities.

At the end of each module, we were given a writing prompt for the writing assignment. Most people chose to continue working on the writing assignments outside of class.

My least favourite module was the bioinformatics one. We had a different instructor for that module and the activities were much less engaging.

Binder:

All of our written work went into a binder that we maintained and added to throughout the term. We were given a few opportunities to hand in our binder for marking and re-marking.

“Evidence worksheets” were only marked for completeness. The problem sets were marked for correctness. Both the evidence worksheets and the problem sets are based off readings which consisted of primary literature, review articles, and less formal news articles/scientific opinion.

Readings:

There are readings to do in this course, but it was not as bad as I expected. I spent an average of two hours a week outside of lecture on this course, mostly on readings or the writing assignments.

Tips:

Since work could be handed and re-handed in at several points throughout the term, I think it is possible to get 100% in the course. It is not difficult to get a grade in the 90s. The most difficult aspect of the assessment were the writing assignments. According to the instructor, perfect marks were given out for the writing assignments only if a new/creative idea was brought up.

Use Zotero for references for the writing assignments. I mentioned it for MEDG 421 above and it is amazing and much better than RefWorks.

For the writing assignments, make sure to have plenty of references for each one. Even better if you reference material outside the required readings.

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Responses

  1. Hi, I was wondering if you had posted your book report for MEDG421 and I’m just not looking at the right places or if you forgot to upload it! :) I’m currently taking MEDG421 and I’m reading the “Emperor of Maladies”, but I’m just not sure what to include in the book report as there was no guideline provided for this year either! :)

    • Hi,

      Yeah I did forget to upload it, along with many other things lol! You can find my book report here, although it’s for a different book: https://idm04.files.wordpress.com/2016/02/book-report.pdf

      I wanted to upload the one with my grade on it, but I don’t have it with me. I think I got something like 80 – 85% on the report.

      • Oh my gosh! Thank you so much! Yeah, I like that it’s for a different book so I don’t feel like I’m taking someone else’s ideas! :P I just needed an idea of what a book report should look like! :) Thank you!

  2. Hey, I’m currently taking stat 302 with eugenia. I’m struggling with the written assignments. Is the difficulty of the midterm and final the same as the written assignments? I’m getting the stuff in lecture and webwork, but I’m totally blanking out when it comes to the written assignments.

    • No, the assignments are definitely harder than the exams, although the exams are more difficult than the webwork. It’s kind of in between webwork and assignments.

      • How did you get through the written assignments? Like what resources did you use besides office hours and textbook? Also any tips on doing well on the exams? Really worried that I won’t pass the final and fail the course ):

        • I actually did not use the textbook at all. I found a partner to work with on the assignments and we would be able to help each other sometimes if one of us got stuck. I also had a third friend in the class that I’d ask help from if I still couldn’t get it.

          There were many times I didn’t really know how to solve the problem on the assignment, but usually I started quite early so I had a lot of time to think about it (even subconsciously). I also reviewed the lecture notes a lot to try and find hints and most of the time that worked out.

          The TA office hours were helpful when I was really stuck. The TA I had gave very strong hints lol. There were some people that went to office hours weekly but I only went there three times, so I do think most of the questions are doable from the lecture notes alone (with some difficulty).

          As for exams, I just went over the assignment/webwork questions and made sure I could do most of them. Also went over the lecture notes problems.

          • I recently just took the midterm and imo it was way too long for a 50min exam. I didn’t do too well either because I had no time to double check my work. Was this the same for you when you took it? Also how was the final compared to midterm and was there scaling done to your final grades?

            • Sorry to hear that… Unfortunately, I don’t really remember the midterm all too well, but I wouldn’t be surprised if mine was also quite long. The final was similar in format to the midterm if I remember correctly, but perhaps more relaxed since we got more time.

              I think there was some scaling. The prof should mention it after it’s been marked.


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