BMI 882, Biomedical data science scholarly literature
University of Wisconsin-Madison
Course meetings: Tu/Thu 8:30-9:20, 4765 Medical Sciences Center
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 (along with its continuation, BMI 882), 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.
- 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.
- The course will be held in-person in 4765 Medical Sciences Center
- COVID-19 vaccination is strongly encouraged
- Use of a high-quality mask is strongly encouraged
- If you have COVID-related symptoms, please stay home
- If you need to miss class, email Karl Broman
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 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.
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:
- Email a PDF or text file to the instructor.
- Post documents to a Box, Google Drive, or DropBox folder that you share with the instructor.
- Post a text or markdown document to a repository at GitHub or Bitbucket.
- Post to a blog, for example with blogdown, GitHub pages, or Wordpress.
For the blog or repository approaches, they should be accessible to the instructor but may otherwise be private.
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:
- Teaching & Learning Data Transparency
- Privacy of Student Records
- Campus Resources for Academic Success
- Course Evaluations and Digital Course Evaluations
- Students’ Rules, Rights, and Responsibilities
- Diversity and Inclusion Statement
- Academic Integrity Statement
- Accommodations for Students with Disabilities
- Academic Calendar and Religious Observances
- SMPH Statement of Non-Discrimination Policy