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13 questions you might have about galaxy

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These slides are adapted from a talk I gave at a Galaxy workshop run by the UC Davis Bioinformatics Core.

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13 questions you might have about galaxy

  1. 1. Keith Bradnam questions you may have about Galaxy 13
  2. 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. 3. 1
  4. 4. How does Galaxy describe Galaxy? “Galaxy is an open, web-based platform for data intensive biomedical research” https://galaxyproject.org
  5. 5. How does Galaxy describe Galaxy? “Galaxy is an open, web-based platform for data intensive biomedical research” https://galaxyproject.org
  6. 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. 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. 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. 9. 2
  10. 10. What is Galaxy? My definition: A web-based platform that provides a simplified interface to many popular bioinformatics tools.
  11. 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. 12. What is Galaxy? My definition: A web-based platform that provides a simplified interface to many popular bioinformatics tools.
  13. 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. 14. What is Galaxy? My definition: A web-based platform that provides a simplified interface to many popular bioinformatics tools.
  15. 15. What is Galaxy? There will only ever be a subset of the currently available command-line bioinformatics tools available in Galaxy.
  16. 16. 3
  17. 17. Who makes Galaxy? Center for Comparative Genomics and Bioinformatics Department of Biology
  18. 18. Who makes Galaxy? Plus countless contributions from the Galaxy community…
  19. 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. 20. Who makes Galaxy?
  21. 21. 4
  22. 22. How long has Galaxy been around? Over a decade!
  23. 23. How long has Galaxy been around? The first publication describing Galaxy: Sep 16th, 2005
  24. 24. How long has Galaxy been around?
  25. 25. How long has Galaxy been around? Total papers over time (cumulative, as of 2015/07)
  26. 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. 27. 5
  28. 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. 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. 30. Will Galaxy be around in 5 years?
  31. 31. 6
  32. 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
  33. 33. 7
  34. 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. 35. 8
  36. 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. 37. Should I learn to use Unix instead? …consider Galaxy as your gateway drug to learning Unix
  38. 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. 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. 40. 9
  41. 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. 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. 43. Can Galaxy be customized? Most Galaxy installations looks very similar, though the colors can also be customized somewhat.
  44. 44. Can Galaxy be customized?
  45. 45. Can Galaxy be customized?
  46. 46. Can Galaxy be customized?
  47. 47. 10
  48. 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
  49. 49. 11
  50. 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. 51. How do I find out more?
  52. 52. How do I find out more?
  53. 53. How do I find out more?
  54. 54. 12
  55. 55. When shouldn’t I use Galaxy? ● People like cakes ● Some people like to bake cakes ● Others buy their cakes from the store
  56. 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. 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. 58. 13
  59. 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. 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. 61. The end

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