This document provides an overview of Galaxy, describing it as a web-based platform for data intensive biomedical research that provides a simplified interface to popular bioinformatics tools. It discusses that Galaxy has been available for over a decade, with ongoing development and contributions from many in the community. While Galaxy can help perform analyses, the user is still responsible for understanding their data and ensuring analyses are set up correctly.

1. Keith Bradnam
questions you
may have about Galaxy
13

2. My spoken commentary
Things that I would normally say when
giving this talk to a real audience are
shown in purple text…like this!

3. 1

4. How does Galaxy describe Galaxy?
“Galaxy is an open, web-based platform for
data intensive biomedical research”
https://galaxyproject.org

5. How does Galaxy describe Galaxy?
“Galaxy is an open, web-based platform for
data intensive biomedical research”
https://galaxyproject.org

6. How does Galaxy describe Galaxy?
Existing tools that you may be familiar
with may not the most appropriate for
working with the extremely large
datasets that genomics generates.

7. 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/

8. 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

9. 2

10. What is Galaxy?
My definition:
A web-based platform that provides a
simplified interface to many popular
bioinformatics tools.

11. What is Galaxy?
● Can run bioinformatics tools
● Can perform basic text manipulations
● Can generate reproducible workflows
● Can also be used as a data hub

12. What is Galaxy?
My definition:
A web-based platform that provides a
simplified interface to many popular
bioinformatics tools.

13. What is Galaxy?
Tools in Galaxy may only provide some
of the options compared to if you ran
the same tool on the command-line.

14. What is Galaxy?
My definition:
A web-based platform that provides a
simplified interface to many popular
bioinformatics tools.

15. What is Galaxy?
There will only ever be a subset of the
currently available command-line
bioinformatics tools available in Galaxy.

16. 3

17. Who makes Galaxy?
Center for Comparative Genomics and Bioinformatics
Department of Biology

18. Who makes Galaxy?
Plus countless contributions
from the Galaxy community…

19. Who makes Galaxy?
GitHub hosts all the code behind
Galaxy and you can see who is making
changes, and you can also raise
bugs/problems yourself!

20. Who makes Galaxy?

21. 4

22. How long has Galaxy been around?
Over a decade!

23. How long has Galaxy been around?
The first publication describing
Galaxy: Sep 16th, 2005

24. How long has Galaxy been around?

25. How long has Galaxy been around?
Total papers over time (cumulative, as of 2015/07)

26. How long has Galaxy been around?
A lot of people have used, and continue
to use Galaxy. It is built up a strong
community of developers and users.

27. 5

28. 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

29. Will Galaxy be around in 5 years?
Tools like iPlant offer a complementary
service to Galaxy. Other tools may also
appear in future.

30. Will Galaxy be around in 5 years?

31. 6

32. 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 a friendly,
graphical user interface

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34. How much does Galaxy cost?
$0.00
Assuming you have access to a web browser and Internet
connectivity, or can install on your own computer

35. 8

36. 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…

37. Should I learn to use Unix instead?
…consider Galaxy as your
gateway drug to learning Unix

38. Should I learn to use Unix instead?
Learning Galaxy will teach you some
concepts which will be useful if you go
on to learn Unix (or Linux).

39. 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

40. 9

41. 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

42. Can Galaxy be customized?
The existence of so many different public Galaxy servers is
a reflection of the demand for custom Galaxy installations

43. Can Galaxy be customized?
Most Galaxy installations looks very
similar, though the colors can also be
customized somewhat.

44. Can Galaxy be customized?

45. Can Galaxy be customized?

46. Can Galaxy be customized?

47. 10

48. 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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50. 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

51. How do I find out more?

52. How do I find out more?

53. How do I find out more?

54. 12

55. When shouldn’t I use Galaxy?
● People like cakes
● Some people like to bake cakes
● Others buy their cakes from the store

56. When shouldn’t I use Galaxy?
Your time may be precious to you.
Learning some bioinformatics can be
useful to appreciate what others could
do for you, i.e. consider outsourcing
your bioinformatics.

57. 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)

58. 13

59. 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

60. Anything else I should know?
Galaxy should be treated like any other
tool you use in science. It will not
magically produce meaningful results for
you. Also, you should document what
you do to ensure that your work is
reproducible by others (and by yourself).

61. The end