Docker hands-on, Nov 9-10, 2015 (intermediate)

Host: C. Titus Brown

Please contact Jessica Mizzi with any questions.

When: Nov 9-10, 2015

Times: 9:15am-4:30pm, both days; people are welcome to drop in when they can.

Where: TBD, but on UC Davis campus somewhere.

Cost: there is no fee.

This workshop is open to everyone, including graduate students, postdocs, staff, faculty, and community members.

Please **REGISTER HERE** if you’re planning on attending any part of this workshop - there are space limits on the room, and this will help us plan coffee as well.

Materials and links from the workshop will be posted to the workshop-specific Hackpad.


  • Monday, 9:15am-noon: Docker overview and introduction. Past workshop materials
  • Monday, 1:30pm-3pm: Introduction to bioboxes. Michael Barton will walk us through the bioboxes ecosystem.
  • The rest of the workshop is unstructured, allowing people to drop in when they have time. We will be covering the planned activities list above depending on the interests of people present. Please come by if you are interested!


This two-day workshop is for exploring the use of Docker containers for running, wrapping, distributing, and publishing scientific workflows. Docker containers provide a lightweight computational framework for all of these things, and we intend that this workshop will provide a friendly and welcoming environment for trying it out.

People new to docker are welcome to attend! We do suggest that attendees have some familiarity with the UNIX command line.

Planned activities:

  • Monday morning will start with an introduction to Docker, using the Amazon cloud to provide a consistent computing environment. You can find the lesson we’ll use, here. People who can’t make Monday morning can run through the tutorial on their own, later, and we’re happy to help!
  • We’ll provide “challenge exercises” for people who want to play with Docker themselves.
  • We’re particularly interested in trying out, which takes a git repo and turns it into a running data analysis environment.
  • We’d like to explore data volumes and the use of Docker for data-intensive research.
  • We’d also like to gain some experience with people installing Docker locally on their Windows and Mac laptops.
  • Bioboxes looks interesting and we plan to play with it!
  • Note this simultaneous workshop in England, the “Bio in Docker” workshop!

Some reading:

Computer requirements

Attendees will need to bring a computer with a Web browser, an Internet connection, and an ssh client; Windows users should install MobaXterm before the workshop.

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