A critical look at what those involved in providing bioinformatics tools and data can learn from YouTube.

1. What can Bioinformaticians
learn from YouTube?

3. Data

4. New project. New schema.

5. EMBL: 20 different data
formats

6. “A biologist would rather share their
toothbrush than their (gene) names”
Mike Ashburner

7. YouTube loves to share

8. 100 million views per day

9. 114 apps

11. <rdf:RDF xmlns=quot;http://www.affymetrix.com/community/
publications/affymetrix/tmsplice#quot;

12. <Gene rdf:about=quot;#1110002A21Rikquot;>
<chr>chr1</chr>
<hasVariant rdf:parseType=quot;Resourcequot;>
<representedBy rdf:resource=quot;#gi13385627quot;/>
</hasVariant>
<hasVariant rdf:parseType=quot;Resourcequot;>
<representedBy rdf:resource=quot;#gi18043402quot;/>
</hasVariant>
<strand>+</strand>
</Gene>

13. RDF, OWL,
SPARQL, GRDDL, WTF?

14. Lower case ‘s’, lower case ‘w’
The semantic web, not
The Semantic Web

15. <tr>
<th class=quot;two-columnquot;>Gene</th>
<td class=quot;two-columnquot;><table width=quot;100%quot; cellpadding=quot;4quot;>
<tr>
<td><strong>
<a href=quot;http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/
get_data.pl?hgnc_id=1101quot;>BRCA2</a></div></strong> (HGNC Symbol)
</td>
<td>
<span class=quot;smallquot;> To view all Ensembl genes linked to the name
<a href=quot;/Homo_sapiens/featureview?type=Gene;id=BRCA2quot;>click
here</a>.</span>
</td>
</tr>
</table><p>
This gene is a member of the Human CCDS set: <a href=quot;http://
www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?
REQUEST=CCDS&amp;DATA=CCDS9344quot;>CCDS9344</a>
</p>
</td>
</tr>

16. <tr class=quot;hgenequot;>
<th class=quot;two-columnquot;>Gene</th>
<td class=quot;two-columnquot;><table width=quot;100%quot; cellpadding=quot;4quot;>
<tr>
<td><strong>
<a href=quot;http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/
get_data.pl?hgnc_id=1101quot; rel=quot;hgnc_namequot;>BRCA2</a></div></strong>
(HGNC Symbol)
</td>
<td>
<span class=quot;smallquot;> To view all Ensembl genes linked to the name
<a href=quot;/Homo_sapiens/featureview?type=Gene;id=BRCA2quot;
rel=quot;gene_listquot; >click here</a>.</span>
</td>
</tr>
</table><p>
This gene is a member of the Human CCDS set: <a href=quot;http://
www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?
REQUEST=CCDS&amp;DATA=CCDS9344quot; rel=quot;ccdsquot;>CCDS9344</a>
</p>
</td>
</tr>

17. Can our web site
be our API?

18. http://www.ensembl.org/Homo_sapiens/geneview?gene=ENSG00000139618

19. http://www.ensembl.org/Homo_sapiens/geneview?gene=ENSG00000139618
my $gene_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Gene' );
my $gene = fetch_by_gene_stable_id( 'ENSG00000139618' );

20. More data on our sites
than through the API
(we’re not the only ones)

21. RSS

22. iCal

23. XML

24. ational state
Represent
transfer
RESTful service

25. psd-production/projects

26. GET
psd-production/projects
RETRIEVE

27. <projects>
project
id type=quot;integerquot;8/id
created-at type=quot;datetimequot;2007-10-22T09:43:30+01:00/created-at
family-id type=quot;integerquot;3/family-id
nameTest BAC/name
updated-at type=quot;datetimequot;2007-10-22T09:43:30+01:00/updated-at
user-id type=quot;integerquot;1/user-id
workspace-id type=quot;integerquot;/
/project
/projects

28. POST
psd-production/projects
CREATE

29. http://psd-production/projects/67

30. http://psd-production/projects/67

31. POST
http://psd-production/projects/67
UPDATE

32. DELETE
http://psd-production/projects/67
DESTROY

33. No installation
No setup
No fancy protocols

34. All you need is curl

35. Perl API

36. Ruby API

37. Tools

38. ows
rkfl
Wo
Tools

39. It’s all about the workflow

40. Trace archive vs SSAHA

41. Workflows are memes
Users add val
ue

42. YouTube knows memes

44. Not invented here!

45. Reproducibility

46. Go with the flow

47. Quickly define workflows

48. Quickly reuse services

49. Data
Explore
Service Service
Data

50. Reuse workflows

51. YouTube for workflows
+
Yahoo! Pipes for
biological data
=
Never having to write
another BLAST parser

52. Design

53. Stop hacking

54. Program to interfaces

55. “The interface is a contract
between data provider and
data consumer”
Lincoln Stein

56. Design for reuse

57. Code for maintenance

58. Foster “accidental
development”
114 YouTube apps

59. However...

60. Designing for reuse is hard

61. With great power comes
great responsibility

62. With great power comes
great responsibility
Available Reliable
Accessible

63. Discoverable:
where is your web site?

64. Design is for humans

65. YouTube is ‘only’ an
online video site

66. A good UI outweighs
smart features

67. “Monolithic solutions
always fail”
Graham Cameron

68. Loose coupling rules

69. Don’t reinvent Eclipse

70. Thank you

71. GREENISGOOD.CO.UK