BMI 881 literature seminar

syllabus

BMI 881, Biomedical data science scholarly literature
University of Wisconsin-Madison
(2 credits)

Course meetings: Tu/Thu 8:30-9:20, 4765 MSC

Instructor: Karl Broman, 6743 Medical Sciences Center

Office hours by appointment

Critical evaluation of the scholarly literature is a crucial skill for researchers. Through this course, Ph.D. students in Biomedical Data Science will develop this valuable skill by focused reading and discussion of a variety of journal articles of present or historical importance the biomedical sciences literature, including biostatistics, biomedical informatics, and relevant topics in statistics and computer science. Students will read and discuss one article or a small group of related articles each week. Students will provide short written summaries in advance of discussion. In addition to the readings and discussion, there will be two written homework assignments related to the articles under discussion. These homework assignments will involve an effort to reproduce the results of an article, the use of computer simulation to investigate properties of methods discussed in an article, or application of the discussed methods to related biomedical data.

Learning outcomes

  • Students will be able to critically evaluate quantitative approaches in the scientific literature.
  • Students will be able to articulate the biological context of a research question and the scientific relevance of analysis results.
  • Students will be able to identify and articulate the strengths and weaknesses of different study designs and analysis methods, including potential biases in research data sets.

COVID-19

  • The course will be held in-person in 4765 MSC
  • COVID-19 vaccination is strongly encouraged
  • Use of a high-quality mask (N95 or KN95) is strongly encouraged
  • If you have COVID-related symptoms, please stay home
  • If you need to miss class, email Karl Broman
  • If you would like to join the class virtually, email Karl Broman in advance so he can arrange a hybrid meeting; the zoom link is on the course canvas site.

Discussion

The primary course activity will be discussion. Be prepared, be engaged, listen, and be respectful.

I ask that everyone strive toward the following:

Norms for discussion

  • Presume positive intentions
  • Engage respectfully
  • Listen attentively
  • Aim for equal participation
  • Respect boundaries
  • Provide evidence

Course grade

Course grade will be based on class participation (40%), written article summaries (30%), and 2 homework assignments (30%).

The article summaries will be scored 0 (missing), 1 (weak), 2 (adequate), and 3 (strong).

The class participation grade will be based on participation in each session, scored according to the following rubric:

Good contributor: Contributions in class reflect thorough preparation. Ideas offered are usually substantive, provide good insights and sometimes direction for the class. Challenges are well substantiated and often persuasive. (Score 3/3)

Adequate contributor: Contributions in class reflect satisfactory preparation. Ideas offered are sometimes substantive, provide generally useful insights but seldom offer a new direction for the discussion. Challenges are sometimes presented, fairly well substantiated, and are sometimes persuasive. (Score 2/3)

Weak contributor: Contributions in class reflect inadequate preparation. Ideas offered are seldom substantive, provide few if any insights and never a constructive direction for the class. Integrative comments and effective challenges are absent. (Score 1/3)

Non-participant: Says little or nothing in class. Hence, there is not an adequate basis for evaluation. (Score 0/3)

Grading scale: 92-100 (A), 87-91 (AB), 82-86 (B), 77-81 (BC), 70-76 (C), 60-69 (D), <60 (F)

Students are encouraged to discuss course content and homework assignments with each other, but the article summaries and homework assignments are to be each student’s own, separate work.

Assignments

Readings

Assigned readings appear in the course schedule. Students are expected to complete the reading assignments in advance of discussion.

Written article summaries

Prior to each Tuesday morning class, write a short summary of the article or articles to be discussed that week: one paragraph summarizing the article(s), and a second paragraph describing your reaction (for example, aspects that you found surprising, interesting, or suspect). The written summary should be less than a page but more than a couple of sentences. Also include two or more discussion questions that might be used to stimulate discussion of the paper.

These article summaries should be completed at least a half-hour prior to the class meeting time. This may be accomplished in a variety of ways. For example:

For the blog or repository approaches, they should be accessible to the instructor but may otherwise be private.

Homework assignments

There will be two written homework assignments related to the articles under discussion. These homework assignments will involve an effort to reproduce the results of an article, the use of computer simulation to investigate properties of methods discussed in an article, or application of the discussed methods to related biomedical data.

Additional policies and statements

Also see the additional institutional policies and statements: