CBB/COMPSCI 662: Computational Systems Biology

The instructor for this course in Spring 2015 is Prof. Alex Hartemink. The teaching assistant is Kaixuan (Kevin) Luo, a CBB graduate student who has previously taken this course and previously served as a TA as well.

The course consists of two major components: executing and presenting a research project in the field as part of a two-person team, and careful reading and discussion of recent primary literature in the field.

Research Project

Each student will work in a two-person team to undertake a research project over the course of the semester. Students should select a partner of their choosing. The best partner is one with whom you can work effectively and diligently. It can sometimes benefit a team to have partners with different backgrounds and expertise, but the opposite is also true, so there is no formal requirement in either direction. Please make use of the provided Google Document to help identify a partner. Teams must be established within one week.

Topic: The project topic should be chosen to be of potential interest in the field. At the same time, it should be of a scope that preliminary results can be obtained within 1–2 months. Having preliminary results early allows time for refinement of methods, further analysis, deeper investigation, and effective writing and communication of ideas.

Deliverables: In addition to a few written progress reports along the way, a draft research paper—written in the style of a scientific paper and carefully edited—will be due on Friday 3 April. The last three class sessions of the semester (7, 9, and 14 April) will be devoted to research presentations by the teams. Presentations should be around 15–20 minutes, and each partner is expected to present in roughly equal measure. The final version of your research paper will be due on Friday 17 April, and represents the final requirement of the course.

Reading Papers

During most class sessions we will discuss a paper from the primary literature. Most of these papers will be extremely recent, so the course is quite different each time it is taught, but each time, it attempts to give students a clear sense of the cutting edge of the field.

For each paper, one student will be designated "Discussion Leader", four to five more students will be designated "Perspective Givers", and the remainder of the class are "Careful Readers".

Roles and responsibilities:

Preparing to lead a discussion:

  1. As mentioned above, be sure to allow sufficient time to understand the paper and its context. The steps that follow cannot be done well without that.
  2. Read this general introduction on leading an effective discussion of a journal article. It isn't tailored exactly to our class setting, but it lays out some general principles as a starting point for the remaining steps below.
  3. Try to identify as many thought provoking questions as you can, especially open-ended interpretative ones that will engender discussion. These should not be focused on background understanding: the hope is that between student initiative to understand the papers, and the cumulative effect of Alex's introductions over the course of the semester, the class will have sufficient background to be ready to engage in a good discussion. Rather, try to think of questions that allow the class to both 1) appreciate the most important and interesting content of the paper, and 2) reflect on how to extend, refine, improve, or build upon the ideas of the paper. You can use the questions of the close readers as inspiration, but don't feel obliged to cover everything they suggest. Consider them as generally representative of what the class might find most productive, but use your own judgment as to how to stimulate the best possible discussion.
  4. Split your questions into those two categories: questions that allow the class to appreciate the most important and interesting content of the paper, versus questions that allow the class to reflect on how to extend, refine, improve, or build upon the ideas of the paper. In each category, order the questions not in terms of where they appeared in the paper, but rather from most interesting/important to least interesting/important. A good discussion can sometimes lead in directions you haven't anticipated, and when those directions are productive, you may not get to all your questions, so you want to be sure that the ones you don't get to are the least interesting/important.
  5. Prepare a handout with your questions to distribute at the start of class. Having a handout allows you to phrase each question precisely, allows you to include figures from another source if that is relevant, allows students to begin pondering questions before you ask them, and allows everyone to leave with something tangible so that they can follow up on questions that we did not have a chance to discuss during class.
  6. On the day of the discussion, try to get more than one response to your questions, but also judge when to move on: decide whether the class is better served lingering on a question or proceeding to the next. Also, it should be noted that sometimes the topic of one of your questions is covered by Alex during the introduction, and in such a case, it's sensible to just skip that question and move ahead to another of your choosing.
  7. Be inclusive of people that have not yet spoken up and invite them to offer their perspective. After an answer, inquire if others in the class have a different perspective. Secret: You actually have to do very little talking if you are well prepared with good questions. Have fun, and try to make sure everyone else has fun, too!