Keynote talk given at the Bioinformatics Open Source Conference at the ISMB in Berlin on 19 July 2013. Discussed from the perspective of Open Source and open definitions how to think about networks and the potential for discontinuities and phase transitions as places where the expansion of networks can lead to significant changes in scientific capacity.

1. http://www.flickr.com/photos/small_realm/6898449633 CC BY
Network Ready Research
The role of Open Source and Open Thinking
BOSC - Berlin - 19 July 2013
Cameron Neylon

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3. Networks.

4. Torres-Sosa et al, doi:10.1371/journal.pcbi.1002669 Waters et al, doi:10.1371/journal.pone.0040337
http://bit.ly/bosc-cn-fig1 http://bit.ly/bosc-cn-fig2

5. Torres-Sosa et al, doi:10.1371/journal.pcbi.1002669 Waters et al, doi:10.1371/journal.pone.0040337
http://bit.ly/bosc-cn-fig1 http://bit.ly/bosc-cn-fig2

6. Torres-Sosa et al, doi:10.1371/journal.pcbi.1002669 Waters et al, doi:10.1371/journal.pone.0040337
http://bit.ly/bosc-cn-fig1 http://bit.ly/bosc-cn-fig2

7. http://commons.wikimedia.org/wiki/File:Arpanet_logical_map,_march_1977.png

8. http://commons.wikimedia.org/wiki/
File:Map_Showing_the_Telegraph_Lines_In_Operation,_Under_Contract,_and_Contemplated_to_Complete_the_C
ircuit_of_the_Globe,_1869.jpg

9. http://commons.wikimedia.org/wiki/File:Post_und_Reisecarte_der_Wege_durch_Frankreich_1703.PNG

11. http://mentionmapp.com

13. Many networks

14. http://www.flickr.com/photos/47691521@N07/6082519811/ CC BY-SA
What can we...

16. Here’s another...

17. 27 January 2009
http://gowers.wordpress.com/

18. 27 January 2009
February 1 2009
http://gowers.wordpress.com/

19. “It is not the case that the aim of the
project is [...to solve the problem...] I think
that the chances of success even for this
more modest aim are substantially less
than 100%.”
Tim Gowers
http://gowers.wordpress.com/2009/02/01/a-combinatorial-approach-to-density-hales-jewett/

20. 27 January 2009
February 1 2009
March 10 2009
http://gowers.wordpress.com/

22. “It feels as though this is to normal
research as driving is to pushing a car.”
Tim Gowers
http://gowers.wordpress.com/2009/02/01/questions-of-procedure/#comment-1701

23. Successful open projects...

24. ...exploit order-disorder transitions

25. ...or...

26. ...network transitions
can be exploited...

27. ...by adopting
open approaches

28. “Open”
is
What
about anyway?

29. http://www.flickr.com/photos/tawheedmanzoor/2309847575 CC BY

30. “Open”
does
What
mean?

31. http://www.flickr.com/photos/yourdon/3088582622
...sharing what we already create

32. The license must not restrict anyone from making
use of the program in a specific field of endeavor.
Open Source Definition - http://opensource.org/osd
The license must not discriminate against any
person or group of persons..
Open Definition - http://opendefinition.org/okd

33. By Open Access we mean...permitting any
users to read, download, copy, distribute,
print, search, or link to the full texts of these
articles, crawl them for indexing, pass them as
data to software, or use them for any other
lawful purpose, without financial, legal, or
technical barriers other than those inseparable
from gaining access to the internet itself.
Budapest Open Access Initiative
http://www.budapestopenaccessinitiative.org/read

34. http://www.flickr.com/photos/mrsdkrebs/6522929727 CC BY

35. http://www.flickr.com/photos/leesean/5114553800 CC BY-SA
For any

36. http://www.flickr.com/photos/fontplaydotcom/2636754594 CC BY

37. “Open”
does being
What
mean?

38. My work can help someone...
http://www.flickr.com/photos/mararie/3313582639/ CC-BY-SA

39. P =
Interest
Friction
x N(help someone)

40. P =
Interest
Friction
x N(help someone)
Proportion that could
use your work
Usability of your work
Number of
people you can
reach

41. Someone out there can help...
http://www.flickr.com/photos/mararie/3313582639/ CC-BY-SA

42. P =
Interest
Friction
x N(getting help)

43. P =
Interest
Friction
x N(getting help)
Proportion that create
work that you can use
Ease of contributing
Number of
people you can
reach

44. P =
Interest
Friction
x N(getting help)
Fixed

45. P =
Interest
Friction
x N(getting help)
As small as possible...

46. P =
Interest
Friction
x N(getting help)
As small as possible...
As large as possible...

47. Being open is acting to reduce
friction and to maximize N...

48. ...for both outgoing and
incoming information...

49. http://www.flickr.com/photos/nanagyei/6744708487 CC BY
Enable forking..

50. http://www.flickr.com/photos/dno1967b/8531643597 CC BY
...and merging

52. What tools...?
http://www.flickr.com/photos/booleansplit/3055314411 CC BY

53. Repositories...

54. ...documentation.

55. ...VMs...

56. ...continuous integration...

57. ...unit tests...

58. ...issue trackers...

59. ...cloud.

60. http://www.flickr.com/photos/drachmann/327122302 CC-BY-SA

61. http://www.flickr.com/photos/robbie73/3387189144 CC-BY-SA

62. http://www.flickr.com/photos/mukumbura/4052671706 CC-BY-SA

63. http://www.software.ac.uk/blog/2013-07-09-recomputation-manifesto

64. http://ivory.idyll.org/blog/vms-considered-harmful.html

65. http://www.flickr.com/photos/marfis75/2459534903 CC BY-SA
Different audiences...

66. http://www.flickr.com/photos/pagedooley/5000489105 CC BY
Different audiences...

67. http://www.flickr.com/photos/9610484@N05/1120115961
...different supports.

68. http://www.flickr.com/photos/soldiersmediacenter/4311667534 CC BY
...different supports.

69. http://www.flickr.com/photos/celebdu/291322346 CC BY
But how do you
support the
unexpected...?

70. http://www.flickr.com/photos/drachmann/327122302 CC-BY-SA

71. http://www.flickr.com/photos/robbie73/3387189144 CC-BY-SA

72. http://www.flickr.com/photos/mukumbura/4052671706 CC-BY-SA

73. If it’s near zero cost...

74. http://www.flickr.com/photos/gaelx/6340466785 CC BY-SA
...and reduces

75. ...or increases
http://www.flickr.com/photos/jennycu/4527765710 CC BY

76. ...then do it.

77. If it costs...

78. http://www.flickr.com/photos/pagedooley/5000489105 CC BY
...but helps a known audience

79. http://www.flickr.com/photos/gaelx/6340466785 CC BY-SA
...and reduces

80. ...or increases
http://www.flickr.com/photos/jennycu/4527765710 CC BY

81. ...for all...

82. ...then do it.

83. Can move it upstream...
http://flickr.com/photos/jason_burmeister/2053139930 CC-BY

84. ...use shared platforms
http://www.flickr.com/photos/37984062@N03/3495256118 CC-BY-SA

85. http://www.flickr.com/photos/mdpettitt/3455884055 CC-BY
...share the load

86. ...then...

87. http://www.flickr.com/photos/mecklenburg/5026128169 CC BY-SA
Something is missing....

88. http://www.flickr.com/photos/beccapeterson/5338013478 CC BY-ND

89. No-one ever got...

90. http://www.flickr.com/photos/natematias/310642831 CC-BY-SA
one of these...

91. ...for infrastructure

92. http://www.flickr.com/photos/joshwept/5689555989/ CC BY

93. Hack the incentives system...?

95. More of the same...?

96. http://www.flickr.com/photos/levork/5026708729 CC BY-SA

97. http://www.flickr.com/photos/yakobusan/2436481628 CC-BY
Community architecture...

98. ...open in the foundations
http://www.flickr.com/photos/56380734@N05/7852142720 CC-BY-SA

99. Reduce friction...
http://www.flickr.com/photos/g_kat26/3535474947 CC-BY-SA

100. ...and support sharing...
http://www.flickr.com/photos/cogdog/5910598311 CC BY-SA

101. http://www.flickr.com/photos/dno1967b/6295812307 CC BY
...but also merging

102. Where are the opportunities?

103. Points of nucleation?
http://www.flickr.com/photos/vitroids/1527109907 CC BY

104. Where are we close
to a phase transition?
http://www.flickr.com/photos/mararie/2185487355 CC BY-SA

105. That’d be a problem for
people who know networks...

106. @cameronneylon
http://cameronneylon.net