A Short Introduction to Galaxy

Contributors

Authors: Saskia Hiltemann Helena Rasche Nicola Soranzo

Questions

• What is Galaxy?

• Why should I use Galaxy?

• How do I use Galaxy?

• How can I connect with the Galaxy Community?

What is Galaxy?

Speaker Notes

What is Galaxy?

Data Intensive analysis for everyone

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• Data Analysis platform
• Web-based
• Easy to use

• Free and Open Source

• Many tools (~9400Galaxy Tool Shed)
• Popular (>11.900 publications)
• Extensive tutorials available

]

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.footnote[Homepage: galaxyproject.org]

Speaker Notes

• 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.

Why use Galaxy?

• It’s easy!
  • No installation, all you need is a browser.
  • No complex commands, just point and click!
• Makes your research reproducible
  • Galaxy keeps track of all analysis details
• Cross-domain: bioinformatics, chemistry, ecology, climate science, ..

Speaker Notes

• 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 web-based user interface to popular data analysis tools.
• This means you don’t have to install anything, just open your browser and go to Galaxy.
• Galaxy also helps you make your research reproducible by keeping track of your analysis steps.
• Galaxy supports many different scientific domains.

How do I use Galaxy?

Speaker Notes

• How do I use Galaxy?

Find a Galaxy server

• UseGalaxy.*: Galaxy Australia (UseGalaxy.org.au), Galaxy Main (UseGalaxy.org), Galaxy France (UseGalaxy.fr), Galaxy Europe (UseGalaxy.eu)

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• Many other smaller, often domain-specific Galaxies available
• List of all public Galaxies (135+): galaxyproject.org/use

Speaker Notes

• 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.
• A lot of universities and other institutions have local private servers.

The Galaxy Interface

• Three main panels
  • Left: Available Tools
  • Middle: View your data and run tools
  • Right: Full record of your analysis history

Speaker Notes

• 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.

Uploading data

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• Upload from your computer

• Import files from URL

• Import from public data stores

  • UCSC, NCBI, ENA, many more..

]

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Speaker Notes

• 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 an Internet 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.

History

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• The history collects all the files of your analysis

• Three buttons
  • galaxy-eye View the file
  • galaxy-pencil Edit attributes
    • e.g. change name
  • galaxy-delete Delete file
• Click to expand
  • file information
    • format, size, ..
  • file preview
  • file options
    • download, visualize, ..

]

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Speaker Notes

• 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.

Finding a tool

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• Explore tool panel sections
• Enter name in Tool search box ]

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• galaxy-star Star you favorite tools to make them easier to find

Speaker Notes

• 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.

Running a tool

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• Choose input files
• Set tool parameters

• Execute

• Below tool form:
  • Help information
  • Tool citation

]

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Speaker Notes

• 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.
• Older versions of a tool are usually kept available to ensure reproducibility.

Analysis Results

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• Tool outputs are added to the history

• Different dataset states
  • waiting , running , success, failed
• Expand for more options
  • galaxy-save Download dataset
  • galaxy-info Information about tool run
  • galaxy-refresh Reload tool with the same parameters
  • galaxy-barchart Visualize dataset
• Red dataset?
  • galaxy-bug Click Bug icon
    • view error message
    • submit error report ]

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Speaker Notes

• 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.

Visualisations

• Galaxy has many options to visualize data

Speaker Notes

• Galaxy offers several ways to visualize your datasets depending on their format.
• For example, protein PDB data can be seen in a 3D viewer.

Multiple Analyses

• Starting a new analysis? Create a new history new-history
• You can have as many histories as you want
• Overview of all your histories galaxy-history
• Good names for your histories help to keep track of your analyses

Speaker Notes

• When you want to start a new analysis, create a new history using the plus icon at the top of the history panel.
• You can always go back to an old history, and there is no limit on the number of histories you can create.
• An overview of your histories is available where you can easily copy files around.
• Copying datasets instead of re-uploading them let you save on your quota.
• Giving your histories good names will help you keep track of your analyses’

Workflows

• Run end-to-end analyses with one click

• Extract from a history
• Build manually with workflow editor
• Import a shared workflow

Speaker Notes

• Workflows let you run your analyses very easily by connecting tools’ outputs and inputs.
• 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 to connect the tools.
• Or you can import a workflow somebody else has shared with you.

Sharing

• You can share everything you do in Galaxy
  • Histories, Workflows, Visualizations
• Sharing options
  • Share with specific users
  • Share via link
  • Publish to make it visible to everybody

Speaker Notes

• 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.

Learning Galaxy

• Galaxy Training Materials (training.galaxyproject.org)

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Speaker Notes

• 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.

Getting Help

• Help Forum (help.galaxyproject.org)

  

• Chat on Matrix

  • Main Chat
  • Galaxy Training Chat
  • Many more channels (scientific domains, developers, admins)

Speaker Notes

• 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 Matrix.

Join an event

• Many Galaxy events across the globe
• Event Horizon: galaxyproject.org/events

Speaker Notes

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

Key Points

• Galaxy lets you perform complex data analysis right from your browser
• These analyses are *reproducible*; Galaxy keeps track of all the details of your analysis
• Galaxy has a very large and active user community
• There are many training materials available to learn Galaxy

Thank you!