1. Cloud BioLinux: pre-configured and on-demand computing for genomics without institutional, geographic or economic boundaries Ntino Krampis, PhD JCVI-NIAID-UL workshop S. Africa 2011

3. example: GS Junior by 454

4. sequencing becoming standard in biology and genetics research

5. besides whole genomes: RNAseq, ChiPseq, and metagenomics 1

7. Problem 1 : sequence data analysis requires high performance

8. and expensive computing hardware

9. Problem 2 : many commonly used bioinformatics tools are difficult to install,

10. usually available only as source code - need technical expertise Acquiring the sequence data is only the first step 2

12. we are all using the cloud: Gmail, Google Docs, Yahoo! Mail, FaceBook; you store and access data on a remote computer

13. cloud computers rented pay-as-you-go by service providers such as Amazon Elastic Compute Cloud (EC2) Solving problem 1: computational capacity on the cloud 3

15. cloud computers cost $0.085 - $2 per hr (max 64GB memory and 8 processors)

16. used by companies that need additional computers without investing on hardware

17. physical locations US East / West regions, EU, Singapore, Japan r esearchers

18. work on the closest location, then distribute results world-wide

19. democratizes access to computing resources outside of institutional, economic or national boundaries 750 hours free for new users! : http://aws.amazon.com/free/ Additional services besides computing and storage : http://aws.amazon.com Additional services besides computing and storage : http://aws.amazon.com 4

21. a VM is uploaded on the cloud; runs using on-demand computing capacity from the EC2 cloud service

22. can be accessed world-wide through a desktop / laptop computer with Internet access

23. removes need for local computing infrastructure at each laboratory How does cloud computing work ? local desktop computers Internet remote Amazon EC2 cloud computing service VM VM VM 5

25. Cloud BioLinux offers a VM on the cloud with 100+ pre-installed and configured bioinformatics tools

26. sequence analysis, de novo assembly, annotation, phylogeny, molecular modeling, gene expression

27. a researcher can initiate a practically unlimited number of VMs for large-scale data analysis Solving problem 2: Cloud BioLinux 6

28. sign- in to the Amazon EC2 cloud control console http://aws.amazon.com/console Username: [email_address] Password: SAcloud! 7 Starting our tutorial: using the cloud

29. Launch Cloud BioLinux through the EC2 cloud console Click the Launch Instance button 8

36. Genbank and Ensembl databases, 1000 human genomes project, influenza

37. data hosted for free, users pay only for the computing time used

38. community program: http://aws.amazon.com/datasets/submit

39. advantage: putting the data where computational capacity is available

40. Amazon EC2 education-research grants: http://aws.amazon.com/education/ Any questions before we get to the exercises ?

42. Connecting remotely to Cloud BioLinux click the NX client icon on your computer's desktop: A. paste the DNS in the “Host” box B. select “Unix”, “Gnome”, remote desktop size C. “ubuntu” is the default user Login “ workshop” is the password we set 16

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45. 19 two S.aureus strains and one S.carnosus species drag & drop the .fna files on the Cloud BioLinux desktop

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57. save and share the Virtual Machine (VM) containing your analysis results with a collaborator storage costs: 0.10$ / GB / month 31

58. authorize access to the VM: public or for certain users other researchers can access the VM with all the software, data, analysis results directly on the cloud Cloud BioLinux: whole system snapshot exchange 32

59. Acknowledgments & Credits Brad Chapman,Tim Booth, Bela Tiwari, Dawn Field – Cloud BioLinux development Deepak Singh and AWS - compute credits on EC2 supporting initial development J. Craig Venter Inst. - sponsorship / time allowed to work on this project D. Gomez, E. Navarro, J. Shao, I. Singh, D. Edwards, M. Stout – JCVI tech innovation Members of the Cloud Biolinux community: Enis Afgan Michael Heuer Richard Holland Mark Jensen Dave Messina Steffen Möller Roman Valls Thank you !