BMI 882 literature seminar

syllabus

BMI 882, Biomedical data science scholarly literature
University of Wisconsin-Madison
(2 credits)

Course meetings: Tu/Thu 8:30-9:20 (via BBCollaborate, in the “Course room” at the Canvas site)

Instructor: Karl Broman

Office hours: Tu 9:30-10:30, Fr 9:30-10:30, or by appointment (via BBCollaborate, http://bit.ly/broman_offhrs)

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.

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.

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

Online working agreements

  • Use your video camera if possible
  • Use names to address each other
  • Use features (mute, raise hand, chat, etc) appropriately
  • Be okay with silence
  • Start and end on time

(taken from The Discussion Project)

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.

Religious observances or other absences

If you need to miss class for religious observances, or any other reason, please let the instructor know in advance, or as soon as is feasible, so that we can try to make some accommodation.

Academic integrity

By virtue of enrollment, each student agrees to uphold the high academic standards of the University of Wisconsin-Madison; academic misconduct is behavior that negatively impacts the integrity of the institution. Cheating, fabrication, plagiarism, unauthorized collaboration, and helping others commit these previously listed acts are examples of misconduct which may result in disciplinary action. Examples of disciplinary action include, but is not limited to, failure on the assignment/course, written reprimand, disciplinary probation, suspension, or expulsion.

Accommodations for students with disabilities

The University of Wisconsin-Madison supports the right of all enrolled students to a full and equal educational opportunity. The Americans with Disabilities Act (ADA), Wisconsin State Statute (36.12), and UW-Madison policy (Faculty Document 1071) require that students with disabilities be reasonably accommodated in instruction and campus life. Reasonable accommodations for students with disabilities is a shared faculty and student responsibility. Students are expected to inform the instructor of their need for instructional accommodations by the end of the third week of the semester, or as soon as possible after a disability has been incurred or recognized. The instructor will work either directly with the student or in coordination with the McBurney Center to identify and provide reasonable instructional accommodations. Disability information, including instructional accommodations as part of a student’s educational record, is confidential and protected under FERPA.

Diversity and inclusion

Diversity is a source of strength, creativity, and innovation for UW-Madison. We value the contributions of each person and respect the profound ways their identity, culture, background, experience, status, abilities, and opinion enrich the university community. We commit ourselves to the pursuit of excellence in teaching, research, outreach, and diversity as inextricably linked goals.

The University of Wisconsin-Madison fulfills its public mission by creating a welcoming and inclusive community for people from every background – people who as students, faculty, and staff serve Wisconsin and the world. https://diversity.wisc.edu