GLBIO 2019, UW-Madison

May 19th, 2019

1:00 pm - 5:00 pm

Instructors: Sarah Stevens

Helpers: Elizabeth McDaniel, Fred Boehm, Sailendharan Sudakaran

General Information

This workshop aims to be the next step in reproducibility for computational biologists and will focus on using and developing software containers. We will review best practices for practicing reproducible research and teach participants how to use Docker, a popular software for containerization (which can also be used by Singularity, another commonly used containerization platform). Using containers can help overcome the many interoperability and dependency issues often encountered when distributing or installing software. Docker images used conjunction with continuous integration is considered to be a possible solution for the reproducibility crisis plaguing research at large. Similar to a Carpentries workshop, a majority of the proposed workshop will be hands-on live-coding. Workshop attendees are expected to have familiarity with the Unix shell and git/github, bring their own laptops, and follow along with the training.

Software Carpentry workshops, in general, aim to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This workshop is an extension of a Softare Carpentry Workshop and aims to teach researchers how to use Docker and the importance of reproducible research. This workshop will briefly review the importance of reproduciblility, and then move the the hands-on portion, learning to make containers in Docker. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers who are attending the GLBIO 2019 conference. You will need to be comfortable using the unix command line and have familiarity with using the version control system git.

Where: Union South, 1308 W Dayton St, Madison, WI 53715. Get directions with OpenStreetMap or Google Maps.

When: May 19th, 2019. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email for more information.


  • Approximate schedule can be found on the docker lesson webpage linked here.
  • There will be a break at about 2:30pm and instead of the last two lessons (cloud and containers from this lesson) we will have some free working time at the end.

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.


To participate in the workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.


See setup page here.