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Written Qualifying Exam (Year 1)

In May of their first year, students are required to take a written qualifying exam to demonstrate proficiency in the fundamentals of bioinformatics and computational biology, as well as competence in synthesizing these fundamentals into original scientific hypotheses or approaches.

The written qualifying exam is scheduled two weeks after the spring (3rd) rotation, in the first part of May. An exam committee consisting of the DGS and BCB faculty with knowledge of the material covered in the module is assembled to create and evaluate the exams. Each committee member is expected to serve at least two consecutive years so that membership can be staggered to maintain consistency and experience among the committee as a whole. The exam comprises four sections relating to broad subject areas:

  1. Dynamic Modeling,
  2. Evolutionary and Functional Genomics
  3. Quantitative Genetics
  4. Structural Bioinformatics.

Each section comprises of two exam questions that are based on a reading list of 2-4 research papers in that subject area. Students are assigned the reading lists for all 8 questions two weeks prior to the exam date. The exam itself is an open-book take-home exam spread over four days. Students are required to complete and submit written answers to 5 of the 8 questions. Exams are graded as either pass or fail. Students who do not pass have the option to take the exam again at the end of their second year. Students who fail a second time are dismissed from the program.

Example material from previous exams

The research articles used in the 2022 written exam were:

  1. Dynamic Modeling (Q1: 27136688, 22218529; Q2: 26479923, 18838440)
  2. Evolutionary and Functional Genomics (Q1: 1560824, 8375663, 26494843; Q2: 34446078)
  3. Quantitative Genetics (Q1: 33712590, Q2: 33200985)
  4. Structural Bioinformatics (Q1: 27151862 , 35332283; Q2: 30568301)

Note: these exam research articles are provided for historical interest only. Be aware that the exam research articles for subsequent exams will be different, potentially substantially so.

Dates for 2023 exam

The dates for the 2023 exam are:

  • Tuesday April 18, 2023: Reading period — students receive journal articles.
  • Tuesday, May 2-5, 2023: Exam period — students receive exam questions, submit answers.

Frequently Asked Questions

Question: Can faculty advisors assist students with their written exam, either in understanding the reading material or answering the questions?

Answer: As a general rule, no.

During the exam period in which students are working on answering exam questions, this would be a clear honor code violation. Students must work alone during that period and, save for communication with the examiners via the student services manager, they must not collaborate with any other person.

During the reading period, students are allowed to discuss the material with their peers, form study groups, etc. However, students’ advisors should not actively participate in such activities, and we recommend against faculty advisors providing any direct help regarding exam reading material, although it is okay to discuss concepts in the abstract, out of the specific context of those papers.

The main reason for limiting or avoiding faculty advisor participation in the reading period is that the written exam is testing the student in skills acquired primarily outside the specific context of their thesis or laboratory; unlike the oral exam, the written exam is not a product of work generated in collaboration with an advisor. Additional reasons for limiting or avoiding faculty participation relate to equity, namely that:

  1. some faculty advisors happen to be more knowledgeable about the areas covered by the exam than others, and this creates or exacerbates potential inequities among students taking the exam;
  2. some faculty advisors are themselves writing one of the exam papers, which puts those advisors in an immediate conflict of interest regarding discussing some of the reading material;
  3. if faculty were able to help students in this way, students of faculty writing parts of the exam would arguably be disadvantaged relative to their peers because there are some research articles their advisors could not discuss.

Question: To what extent are students allowed to collaborate during the reading period?

Answer: Students are allowed to discuss the material with their peers, form study groups, etc. Collaboration during this period should be limited to discussion, whether this is verbal, as written conversations, or the use of explanatory tools such as illustrations/diagrams. It should not extend to collaborating on the formulation of, eg, pre-prepared written answers to likely questions or computer code that may be deployed during the exam. The work by each individual during the exam period must be their own, and this is violated by any direct use of pre-prepared, group materials.