The document outlines resources for utilizing Amazon Web Services (AWS) in bioinformatics, emphasizing automation, ease of use, and community-driven frameworks. It highlights tools like CloudBioLinux and CloudMan for creating customizable and sharable cloud computing environments for scientific workflows. Additionally, it provides a step-by-step guide on setting up instances and running analysis pipelines through web interfaces.

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