Fork our course: A semester-long Data Carpentry course for biologists

This is post is co-authored by Zack Brym and Ethan White

Over the last year and a half we have been actively developing a semester-long Data Carpentry course designed to be easily customized and integrated into existing graduate and undergraduate curricula.

Data Carpentry for Biologists contains course materials for teaching scientists how to work more effectively with data. The course provides introductions to data management and relational databases, data manipulation and analysis, and data visualization. It covers the same general types of material as a two-day Data Carpentry workshop, but expands the materials and opportunities for practice into a full-length university course. The teaching material uses R and SQLite, with some corresponding materials for Python as well. To help students understand the direct applications to their interests, the examples and exercises focus on biological questions and working with real data. The course emphasizes using best practices to produce reusable and reproducible data analysis.

Active-learning Teaching Materials

Learning computing requires active practice by working through programming problems. Just diving in to computing is challenging for most scientists, so the course instruction is designed to combine short live-coding introductions to concepts followed immediately by the students working on a related exercise. Additional exercises are assigned later for practice. This follows the “I do”, “We do”, “You do” approach to teaching, which leverages the benefits of active-learning and flipped classrooms without leaving students who are less comfortable with the material feeling lost. The bulk of class time is spent working on assigned exercises with the instructor moving around the room helping guide students through things they don’t understand and engaging with students who are thinking about advanced applications of what they’ve learned.

This approach is the result of lots of reading about effective teaching methods and Ethan’s experience teaching this and related courses over the last six years at Utah State University and the University of Florida. It seems to work well for both students that get the material easily and those that find it more challenging. We’ve also tried to make these materials as useful as possible for self-guided students.

Open course development

Software Carpentry and Data Carpentry have shown how powerful collaborative lesson development can be and we’re interested in bringing that to the university classroom. We have designed the course materials to be modular and easy to modify, and the course website easy to clone and set up. All of the teaching materials and associated website files are openly available at the Data Carpentry for Biologists repository on GitHub under CC-BY and MIT licenses. The course materials are all written in Markdown and everything runs on Jekyll through GitHub Pages. Making your own version of the course should take less than an hour. We’ve developed documentation for how to create your own version of the course and how to contribute to development. Exercises and assignments are modular and changing exercises and assignments simply involves reordering items in a list. Adding a new exercise involves creating a new Markdown file and then adding its title to the list of exercises for an assignment.

Get Involved

If you teach, or want to teach, a course like this, we’d love to get you involved. Here are some useful links for getting started.

–   I want to teach the course.
–   I have some feedback.
–   I want to contribute to the project.

We want to be sure getting involved is as easy as possible. We’ve worked hard to provide documentation and help resources for students and instructors. Students can find all they need to know at our student start guide. Instructors have access to course content and site design documentation.

If your having trouble finding something or getting something to work, or simply have some feedback about the course please open a new issue at GitHub or send us an email.


Development of this course was generously support by  the Gordon and Betty Moore Foundation’s Data-Driven Discovery Initiative through Grant GBMF4563 to Ethan White and the National Science Foundation as part of a CAREER award to Ethan White.

6 Comments on “Fork our course: A semester-long Data Carpentry course for biologists

  1. Thanks for making all this available, Zack and Ethan! I’ve already forked it to develop a website for general ecology course ( It’s still in the works, so about 2/3 of the links still go to DataCarpentry material. I couldn’t have started to put something like this together without your template. Thanks! And, good work.

  2. That’s awesome to hear Andrew! Thanks for letting us know and let me know if there’s anything we can do to help.

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  5. This is great! Next fall, I am going to teach a (new) course to 1st year Bachelor Biology students that has teaching them python as a component. I am on the lookout for exercises to reuse. Even though you don’t maintain them anymore, I already found many useful python exercises in your material!

  6. That’s great to hear! We’re certainly open to doing basic maintenance, fixing bugs, merging PRs, etc. on that material, so if you see any improvements that can be made we’d love to hear about them. If course name, number, website at some point we’d also love to add it to the list of courses that are using the material.

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