Life science research, data platforms and cloud computing

1. Platforms for data science
Deepak Singh, Ph.D.
Amazon Web Services
Data transmission for international genomics projects 2010

2. the new reality

3. lots and lots and lots
and lots and lots of data

4. lots and lots and lots
and lots and lots of
people

5. lots and lots and lots
and lots and lots of
places

6. constant change

7. science in a new reality

8. science in a new reality
^

9. data
science in a new reality
^

10. data as a
programmable resource

11. versioning

12. provenance capture

13. filter

14. aggregate

15. integrate

16. extend

17. mashup

18. automate

19. human interfaces

20. tough problem

21. really tough problem in
the new reality

22. goal

23. optimize the most
valuable resource

24. compute, storage,
workflows, memory,
transmission, algorithms,
cost, …

25. people
Credit: Pieter Musterd a CC-BY-NC-ND license

26. enter the cloud

27. what is the cloud?

28. infrastructure

29. scalable

30. highly available

31. dynamic

32. extensible

33. secure

34. a utility

35. programmable

36. class Instance
attr_accessor :aws_hash, :elastic_ip
def initialize(hash, elastic_ip = nil)
@aws_hash = hash
@elastic_ip = elastic_ip
end
def public_dns
@aws_hash[:dns_name] || ""
end
def friendly_name
public_dns.empty? ? status.capitalize : public_dns.split(".")[0]
end
def id
@aws_hash[:aws_instance_id]
end
end

37. include_recipe "packages"
include_recipe "ruby"
include_recipe "apache2"
if platform?("centos","redhat")
if dist_only?
# just the gem, we'll install the apache module within apache2
package "rubygem-passenger"
return
else
package "httpd-devel"
end
else
%w{ apache2-prefork-dev libapr1-dev }.each do |pkg|
package pkg do
action :upgrade
end
end
end
gem_package "passenger" do
version node[:passenger][:version]
end
execute "passenger_module" do
command 'echo -en "nnnn" | passenger-install-apache2-module'
creates node[:passenger][:module_path]
end

38. a data science platform

39. dataspaces
Further reading: Jeff Hammerbacher, Information Platforms and the rise of the data scientist, Beautiful Data

40. accept all data formats

41. evolve APIs

42. beyond the database
and the data warehouse

43. move compute to the
data

44. data is a royal garden

45. compute is a
fungible commodity

46. “I terminate the instance
and relaunch it. Thats my
error handling”
Source: @jtimberman on Twitter

47. the cloud is an
architectural and
cultural fit for
data science

48. amazon web services

49. your data science platform

50. s3://1000genomes

51. Credit: Angel Pizzaro, U. Penn

52. http://usegalaxy.org/cloud

53. mapreduce for
genomics
http://bowtie-bio.sourceforge.net/crossbow/index.shtml
http://contrail-bio.sourceforge.net
http://bowtie-bio.sourceforge.net/myrna/index.shtml

55. AWS knows massively
scalable infrastructure

56. you know the needs of
the science

57. we can make this work
together

58. deesingh@amazon.com
Twitter:@mndoci
http://slideshare.net/mndoci
Inspiration and ideas from
Matt Wood, James Hamilton
& Larry Lessig
Credit” Oberazzi under a CC-BY-NC-SA license