Originally given at RailsConf, this talk outlines how the Wellcome Trust Sanger Institute is using Ruby and Rails as part of their new sequencing platform.

1. Genomes on Rails
has_many :sequences

2. Hello

3. ➊
Previously
➋
Production
➌
Process

4. ➊ Previously

5. The human genome
15 years to decode
3 billion letters

6. $3 billion

7. $3 billion ++

8. Race for the prize

11. Open data

12. Open source

13. Perl

14. Lots of Perl

15. Lots of Perl
~4500 modules

16. Onwards!

17. 40 species

21. Map evolutionary
space

22. Compare genomes

23. compare species
Compare genomes

24. compare species
Compare genomes
compa re indi viduals

25. More Perl
~1500 modules

29. Quantum leap!

30. 1000 personal
genomes

31. beyond 23andme
1000 personal
genomes

32. Hypertension

33. Diabetes

34. Coronary heart disease

35. Bipolar disorder

36. Malaria

37. ➋ Production

38. Register projects
Register samples
Sample prep
Sequencing
Analysis

42. Change!

43. Flexible data capture

44. Virtual fields

45. Sample
Name
Organism
Concentration

46. class Sample < ActiveRecord::Base
has_many :descriptors
has_many :descriptor_values
end

47. Key value pairs

48. Faster than you’d think

51. Change!

52. V1 V2
Sample Sample
Name Name
Organism Organism
Concentration Concentration
Origin
Quality metric

55. Rationalize!

56. V1 V2
Sample Sample
Name Name
Organism Organism
Concentration Concentration
Origin
Quality metric

57. Mapping!

58. V1 V3
Sample Sample
Name Name
Organism Species
Concentration Concentration
Origin Origin
Quality metric

59. Pipeline management

60. Workflow
Task 1 Task 2 Task 3
Name Name Name
Operator Serial number Passed
Instrument Kit

64. Throughput!

66. 320Tb 450 CPU

67. 320Tb 450 CPU Archive

68. 75 Tb

73. pilot study!

74. Multiple apps

75. Multiple instances

76. Loosely coupled

77. Loose coupling is hard

78. Deployment

79. Maintenance

80. Monitoring

81. Hard to maintain
separation

82. Support novel science

83. Single code base

84. nginx reverse proxy

85. fairnginx

86. Mongrel

87. Fast deployment

88. Automate everything

90. Play well with others!
Interoperability!

91. Legacy databases

92. RESTful services

93. Generate API stubs

95. SCALE!

96. Trillionics

97. 2 X

98. 150Tb per week

99. Over 6 months

100. More hardware

101. 400 additional nodes

102. additional 360 Tb

103. Towards a
Virtual Institute

104. Lots of data

105. Lots of data, lots of
people

106. Lots of data, lots of
people, lots of compute

107. Lots of data, lots of
people, lots of compute,
lots of uses

108. Lots of data, lots of
people, lots of compute,
lots of uses, lots and lots
and lots and lots...

109. ➌ Process

110. Concept Requirements Development Product

111. takes too lon
g
Concept Requirements Development Product

112. takes too lon
g
Concept Requirements Development Product
the se change

113. Plan Development
REVIEW Concept
What we need Get ready

114. Focused

115. Project owner is key

116. Weekly releases

117. More flexible

118. Less time

119. Better transparency

120. Less software

121. Sequencing informatics

122. Thank you

123. GREENISGOOD.CO.UK