Walk through using CloudBioLinux, CloudMan, BioCloudCentral to do custom biological analyses on Amazon EC2 hardware.

1. Amazon resources for bioinformatics
Brad Chapman
Bioinformatics Interest Group, 18 Oct 2012

2. Goals
Automate:
Reduce steps
Remove activation energy
Increase abstraction
Improve:
Sharing
Reproducibility
Teaching

3. Installation

4. Easier installation

5. No installation

6. Challenge
Biology computing platform
Widely accessible
Customizable
Community driven

7. General cloud frameworks
http://aws.amazon.com/

8. Not only Amazon
http://gigaom.com/cloud/what-google-compute-
engine-means-for-cloud-computing/

9. CloudBioLinux
Amazon image with bioinformatics software and
libraries
Automated build framework
Community eort to maintain and extend
http://cloudbiolinux.org

10. CloudMan
SGE cluster plus automation
Web interface and monitoring
Persistence and sharing
Powers the Galaxy Cloud oering
http://usecloudman.org/

11. BioCloudCentral
Automate setup of Amazon instance
Launch CloudBioLinux and CloudMan
Provide easy ssh access, no key pairs
http://biocloudcentral.org

12. Galaxy
http://usegalaxy.org

13. Acknowledgments
CloudBioLinux: Ntino Krampis, Tim Booth,
Dawn Field, Pjotr Prins, John Chilton and
CloudBioLinux community.
CloudMan: Enis Afgan, James Taylor
BioCloudCentral: Enis Afgan, John Chilton,
Dannon Baker

14. Documentation
http://cda.currentprotocols.com/WileyCDA/CPUnit/
refId-bi1109.html

15. What we'll do
1 Sign up for Amazon
2 Start a CloudBioLinux/CloudMan instance
3 Add nodes to create a compute cluster
4 Run variant calling pipeline
Everything done through the web

16. Getting started
Sign up for Amazon Web Services
http://aws.amzaon.com
Get security credentials: Access Key and Secret Key
http://portal.aws.amazon.com/gp/aws/
securityCredentials

17. Launch: http://biocloudcentral.org

18. Ready two minutes later

19. Login to CloudMan

20. Shared CloudMan images
Package a complete analysis environment
Data
Customizations
Sharable with other users
Share string with NGS analysis platform:
cm-b53c6f1223f966914df347687f6fc818/shared/2012-07-23--19-23/

21. Start CloudMan

22. CloudMan console

23. CloudMan admin page

24. CloudMan: managing a cluster

25. Associated Galaxy instance

26. Analysis data on shared instance

27. Graphical variant-calling pipeline

28. Analysis data linked to pipeline

29. Congure pipeline

30. Run pipeline

31. Shut everything down

32. What happened
1 Sign up for Amazon
2 Start a CloudBioLinux/CloudMan instance
3 Add nodes to create a compute cluster
4 Run variant calling pipeline
Everything done through the web

33. ssh to the machine
$ ssh ubuntu@184.73.104.51
ubuntu@184.73.104.51's password:
Welcome to Ubuntu 12.04 LTS
(GNU/Linux 3.2.0-23-virtual x86_64)
ubuntu@ip-10-72-197-11:~$

34. NX graphical client: login
http://www.nomachine.com/download.php

35. NX graphical client: desktop

36. Summary
Use cloud resources to build:
Machines with standard software
Cluster management
Analysis pipelines
Reproducible, sharable instances
Web-based interfaces