Best Practices for Teaching

Use the Best Compute Platform

The Computing Platforms page includes options and recommendations for computing backends with which to teach Galaxy.

Use Galaxy's Built-In Mechanisms

Galaxy has several mechanisms that make teaching Galaxy and bioinformatics easier. Using these capabilities during a workshop or course is a natural way to demonstrate them.

Published histories, workflows, and visualizations

Pre-populate teaching Galaxy instances with published histories, workflows, and visualizations that users can refer to for guidance or import into their workspace. Published objects can be easily accessed under the Shared tab on all Galaxy instances.

Data libraries

Avoid training-time dependencies on external resources (that may be down during training) and swamping your local network by pre-loading data into Data Libraries on the training server. To do this, you will need either admin access to the server or the cooperation of the server's admin. For more details on how to become a Galaxy admin, check out this guide.


License all materials under CC-BY to makes things much easier.

Use Established Training Techniques

General best practices

Below are a list of best practices that may be helpful for any Galaxy training session.

Start with a specific exercise

Start with an exercise where users are told exactly what to do. Then, open it up to give users an opportunity to try things for themselves.

Introduce conceptually simple material when covering NGS

Start with assembly and/or mapping exercises. These concepts are typically easier for new users to understand than, for example, a complex RNA-Seq or ChIP-Seq analysis workflow.

Let the users be teachers

Structure a course by pairing one user with a computing background and one user with a biological or medical background. This pairing allows biologists to pick up general computer interaction skills and computer scientists to gain an appreciation for the motivation behind a particular analysis.

Utilize skills of computer scientists

Ask tech- or computer-savvy users to be teaching assistants. They may not be familiar with Galaxy or the biology, but they are familiar with computers and are already aware that cAsE may matter, for example, or that tabs and spaces are treated differently.

Create online communities

Set up a mailing list or Google Group for every training session. Establishing a network for users who know each other offers a much less intimidating environment than public boards.

Workshop-specific best practices

Below are a list of best practices that may be helpful when doing a workshop where you only have a limited number of hours or days to teach the material, and you are always in the classroom with the users.

Course-specific best practices

Below are a list of best practices that may be helpful when teaching an academic course using Galaxy. In this case, users may be using Galaxy in a lab and for homework, but there are also contact hours where hands-on exercises are not the focus.