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What is Galaxy? And why should I learn it? Keith Bradnam
What is Galaxy?And why should I learn it?
Keith Bradnam
questions you may have about Galaxy13
1
How does Galaxy describe Galaxy?
“Galaxy is an open, web-based platform for data intensive biomedical research”
https://galaxyproject.org
How does Galaxy describe Galaxy?
“Galaxy is an open, web-based platform for data intensive biomedical research”
https://galaxyproject.org
How does Galaxy describe Galaxy?
“Galaxy is an open, web-based platform for data intensive biomedical research”
https://galaxyproject.org
How does Galaxy describe Galaxy?
“Galaxy is an open, web-based platform for data intensive biomedical research”
https://galaxyproject.org
Microsoft Excel is not always the right tool for the job
Microsoft: “By importing FASTA data into Excel, researchers are better able to visualize and analyze information.”
https://www.flickr.com/photos/msr_redmond/
Microsoft Excel is not always the right tool for the job
Microsoft: “By importing FASTA data into Excel, researchers are better able to visualize and analyze information.”
https://www.flickr.com/photos/msr_redmond/
X
2
What is Galaxy?
● A web-based platform that provides a simplified interface to many popular bioinformatics tools.
● Can generate reproducible workflows
● Can also be used as a data hub
What is Galaxy?
● A web-based platform that provides a simplified interface to many popular bioinformatics tools.
● Can generate reproducible workflows
● Can also be used as a data hub
What is Galaxy?
● A web-based platform that provides a simplified interface to many popular bioinformatics tools.
● Can generate reproducible workflows
● Can also be used as a data hub
3
Who makes Galaxy?
Center for Comparative Genomics and Bioinformatics
Department of Biology
Who makes Galaxy?
Plus countless contributions from the Galaxy community…
Who makes Galaxy?
4
How long has Galaxy been around?
Over a decade!
How long has Galaxy been around?
1st publication describing Galaxy: Sep 16th, 2005
How long has Galaxy been around?
How long has Galaxy been around?
5
Will Galaxy be around in 5 years?
● A good question to ask!
● Should be safe to use for analysis of your next paper or two…
● …but can always be useful to stay alert for alternatives that might emerge
Will Galaxy be around in 5 years?
6
How is Galaxy different from Unix?
● Unix is vastly more powerful…
● …but comes with a steeper learning curve
● For many bioinformatics tools, Galaxy is simply wrapping those tools in some friendly, child-proof packaging
7
How much does Galaxy cost?
$0.00Assuming you have access to a web browser and Internet connectivity, or can install on your own computer
8
Should I learn to use Unix instead?
● If you can, yes.
● Unix has been around for almost 50 years, not going to disappear any time soon.
● You will be able to do many more powerful things if you learn to use Unix, but…
Should I learn to use Unix instead?
…consider Galaxy as yourgateway drug to learning Unix
Should I learn to use Unix instead?
● Galaxy will teach you about command-line options of bioinformatics tools
● Galaxy will show you some simple ways of processing text files
● Galaxy will teach you the idea of building reproducible workflows
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Can Galaxy be customized?
● Yes. Many customizations can be made
● Some Unix expertise needed
● Common customizations add specific bioinformatics tools and/or prepopulate Galaxy with specific datasets
Can Galaxy be customized?
The existence of so many different public Galaxy servers is a reflection of the demand for custom Galaxy installations
Can Galaxy be customized?
Can Galaxy be customized?
Can Galaxy be customized?
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Why should I learn Galaxy?
● To perform powerful bioinformatics analyses
● To perform reproducible bioinformatics analyses
● To dip your toes into the world of computing
● Because Microsoft Excel is not the answer
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How do I find out more?
● Try the main Galaxy server:○ https://usegalaxy.org
● Galaxy wiki:○ https://wiki.galaxyproject.org
● Biostar forum○ http://biostar.usegalaxy.org
● Mailing lists
How do I find out more?
How do I find out more?
How do I find out more?
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When shouldn’t I use Galaxy?
● People like cakes
● Some people like to bake cakes
● Others buy their cakes from the store
When shouldn’t I use Galaxy?
Paying a bioinformatics core facility to do your analysis may be a better use of your money (and time)
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Anything else I should know?
● Galaxy will not do your work for you
● Galaxy will not write papers for you!
● Remember the bioinformatics maxim:○ Garbage in → Garbage out
The end
