What is Galaxy?

• Galaxy is a web based data analysis platform.
• It is easy to use, and completely free.
• Galaxy offers over eight thousand analysis tools.
• Galaxy is widely used. It currently has over ten thousand publications.

• Data analysis can be very complex.
• It often requires specialized programming knowledge or command line skills.
• Galaxy makes this a lot easier by providing a graphical user interface to popular data analysis tools.
• Galaxy is web based. This means you don't have to install anything, just open your browser and go to Galaxy.
• Galaxy supports many different scientific domains.

• How do I use Galaxy?

• There are three main Galaxy servers. Galaxy Main, Galaxy Europe, and Galaxy Australia.
• These three Galaxies have the biggest teams behind them, and offer the most tools and resources.
• You can register an account for free on any of these servers.
• In addition, there are many smaller galaxy servers to choose from.
• Many of these are domain specific. For example, Galaxy proteomics focuses on proteomics tools and workflows.

• The Galaxy user interface consists of three main parts.
• On the left is the list of available tools.
• In the middle panel you will run your analysis tools and view your data and results.
• On the right is a full record of your analysis history.

• The first step of an analysis is to get your data into Galaxy.
• This can be done in several ways.
• You can upload files from your computer.
• Or you can enter a URL, and Galaxy will download the data for you.
• Furthermore, Galaxy can import data directly from many online data stores such as UCSC, NCBI, and many more.

• All files you upload will appear in your history.
• There are 3 button on each dataset in your history.
• The eye icon lets you view the dataset. This will show up in the middle panel of Galaxy.
• The pencil icon allows you to edit the attributes of the file. For example you can change the file name here.
• The cross icon lets you delete the dataset from your history.
• You can also click on the dataset to expand it. This will show more information and more options.

• After your data is uploaded, you are ready to run tools.
• You can find tools by exploring the tool list on the left.
• If you already know the name of the tool you want to use, you can enter this in the search box at the top of the tool panel.
• If you have found a tool you like, you can add it to your favorites by clicking the star at the top of the tool.

• When you click on a tool, it will show up in the middle panel.
• Here you can select your input files and set the parameters for the tool.
• Then you can hit the execute button to start the tool.

• The results of the analysis will be added to your history.
• You will see these output files go through various states.
• When a dataset is grey, it means it is waiting to run.
• When it turns orange, it means the tool is running.
• When the tool is finished, the outputs will turn green if the tool ran successfully.
• You can then click on the history item to get more information and options.
• For example, you can download the file to your computer.
• Or you can reload the tool with the same parameters.
• There is also an option to visualize your data.
• If there was a problem with the tool, it will turn red.
• You can click on the bug icon to view the error message or submit a error report to the Galaxy administrators.

• Galaxy also has many options to visualize your datasets.
• Depending on the data type, there will be different visualisation options.

• When you want to start a new analysis, you can create a new history using the plus icon at the top of the history panel.
• You can have as many histories as you want.
• You can easily switch back and forth between histories.
• Giving your histories good names will help you keep track of your analyses'

• Workflows let you run your analyses very easily.
• There are multiple ways to create a workflow.
• Workflows can be automatically extracted from a history.
• This means you perform the analysis manually once, and then can easily repeat it on different input data.
• You can also build workflows by hand using the workflow editor.
• Or you can import a workflow somebody else has shared with you.

• Everything you do in Galaxy can be shared.
• You can share your history, your workflow, and your visualizations.
• There are different ways to share your work.
• You can either share it with specific Galaxy users.
• Or you can get a share link that you can send to anybody.
• If you publish your work, it will be visible to everybody.

• If you would like to learn more about Galaxy, there are a large number of tutorials available.
• These tutorials cover a wide range of scientific domains.

• If you get stuck, there are ways to get help.
• You can ask your questions on the help forum.
• Or you can chat with the community on Gitter.

• There are frequent Galaxy events all around the world.
• You can find upcoming events on the Galaxy Event Horizon.