Here is a brief description of my plans for a Reproducible Research course. This experimental course will be completely online and use free, online tools. Please let others know about this class. I need enough interest to get this thing running regularly. The information below is provisional, and may be changed by the time the course actually runs. The course is now running for the first time!

Catalog Description

A comprehensive course in reproducible research methods as applied to biological problems. Data management, manipulation, and analysis are emphasized using free and open-source software programs. No prior background in programming is required.

Typically Offered: Fall, Spring, Summer


BIOL 121, MATH 120

Required Materials

  • Textbook: None. All readings will be from free, online sources and linked to from the Blackboard shell.

  • Computer: You will need a computer with a reliable internet connection to complete this course. Approved operating systems include Windows, Macintosh, and Linux. You could possibly use a Chromebook, but you would need to spool up a virtual private server (on AWS, Azure, DigitalOcean, etc.) to complete much of the work.

Course-Specific Learning Outcomes

There are several course-specific outcomes for students in this class, as described below. By the conclusion of this course, successful students should be able to:

By the completion of this course, students will:

  1. Create well-structured databases of biological information;

  2. Design reasonable experiments to address specific scientific hypotheses;

  3. Write computer programs in R to analyze biological data;

  4. Demonstrate the best practices of reproducible research while using appropriate scientific software.

  5. Work collaboratively with others to apply data management and analysis concepts while investigating and reporting upon a biological question.


All five course outcomes will be evaluated using assignments, live coding exercises, and a collaborative course project. The assignments represent the work of individuals. They include short essays, problem solving, and short coding projects wherein students address novel biological problems using the software and content presented in class (40% of the final grade). Live coding exercises are done synchronously online using Zoom. Students demonstrate solutions to problems presented by the instructor (individually or in small groups) in real time. This is more of a Socratic method to teaching and learning (20% of the final grade). The final projects allow students to apply all that they have learned about reproducible research while working collaboratively with a few of their classmates (group size will typically be four students). The students will gather and clean biological data, analyze and evaluate its meaning, and report their findings to the entire class using Zoom. A scoring rubric will be used to evaluate each student’s contribution and the quality of the final report (40% of the final grade).

Sample Syllabus

As this course as has not yet run, there is not a syllabus available. When I get one put together, I will post a copy here. Once posted, you may use this document to gauge how I approach the course topics and assess student learning. Nota bene: future syllabi (or those from other instructors of this course) may differ substantially.

On-line Course Materials

This class is taught as a completely course using our course management system, Blackboard and GitHub. Blackboard will be used to provide:

  • A PDF copy of the current course syllabus.

  • A posting of all course announcements

  • A calendar of all course assignments and deadlines.

  • On-line access to your course grades.

  • E-mail and chat interfaces to contact me about the class.

  • A bulletin board for on-line class discussions as well for answering any questions or comments that you might post.

  • A search tool to allow you to find material in the site.

The GitHub materials will include all of the course materials, assignments, and projects for the semester.

Please feel free to contact me if you have any questions, comments, or concerns about this course. Thanks!

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