Cloud BioLinux provides pre-configured virtual machines on Amazon EC2 with over 100 bioinformatics tools for genomic analysis. It allows small labs and researchers to perform large-scale genomic computations in the cloud without extensive hardware, expertise, or time to install software locally. The Cloud BioLinux virtual machine images can be run on EC2 or other cloud platforms like Eucalyptus. The project is open source and community-driven to expand available tools and collaboration capabilities.

1. Cloud BioLinux: Pre-Configured and On-Demand
High Performance Computing for the Genomics Community
Ntino Krampis, PhD
Next-Gen Sequence Data Management '10
Providence, RI

2. Expensive sequencing, computing and large organizations
●
multi-million, broad-impact sequencing projects
● large sequencing center, with a dedicated bioinformatics department
● large-scale computations on SGE cluster, algorithm acceleration hardware

3. Bench-top, commodity sequencing and small labs
●
small-factor sequencer available: GS Junior by 454
● sequencing as a standard technique in basic biology and genetics research
● remember microarrays and lengthy assays for protein interactions ?
● RNAseq and ChiPseq, and each biologist will be tackling a metagenome

4. Will small labs become the long tail of sequencing ?
amount of
sequencing Credit: WikiMedia Commons
number of labs
● downstream bioinformatic analysis required for biological discovery
● basic analysis example: large-scale BLAST to public DBs (try 0.5GB at NCBI)
● do not have the hardware, expertise, or time to install and run software locally

5. Cloud Biolinux
pre-configured and on-demand bioinformatics on the cloud
● a public virtual machine (VM) on EC2 with 100+ bioinformatics tools
● how it came to be, what offers for sequence analysis
● where and how do I run it, especially if I am not a computer expert
● modifying and sharing VM configurations and data with your peers
● openness and community around Cloud Biolinux

6. Cloud Biolinux
The Biolinux part
● an Ubuntu Linux desktop for bioinformatics
tinyurl.com/BioLinux-NEBC ● NEBC packaged software and maintains repository
+ ● Ubuntu AMI on EC2, pull packages from repository
● additional software of interest to JCVI
=
tinyurl.com/CloudBioLinux-JCVI

7. Cloud Biolinux
what comes in the box
● glimmer, hmmer, phylip, rasmol, genespring, clustalw, EMBOSS
● mpiBLAST clusters using EC2 virtual machine instances
● Celera whole genome shotgun assembler
● NX remote desktop, easy to use for benchtop scientists

8. Cloud Biolinux
The Cloud part
● find our VM on Amazon EC2:
Biolinux 5.0 packages (32-bit): ami-6953b200
Biolinux 6.0 packages (64-bit): ami-6011e409 , EBS based
● 17GB / 6 core instances 0.5$ / hour, see aws.amazon.com/ec2/pricing
● a small bacterial genome assembly costs a little over 2$
● up to 68 RAM / 26 core, EBS up to 1000 GB in size (0.10$ / GB / month)
● make a copy of our public Biolinux ami - add your data - make private

9. Cloud Biolinux
http://tinyurl.com/cloud-biolinux-tutorial (credit to the NEBC team)
simply signup at
aws.amazon.com
then
aws.amazon.com/console
and

10. Cloud Biolinux
http://tinyurl.com/cloud-biolinux-tutorial (credit to the NEBC team)
●find Cloud Biolinux
AMI using ID
● enter desired password
for remote desktop login
● all other default

11. ●get remote desktop client:
nomachine.com/download.php
●simply enter VM's IP address
and your password

13. What if I want to share my
alignments with a collaborator?
save your data as a new AMI
EBS cost 0.10$ / GB / month
at 15GB, it costs 1.5$ / month

14. share your data: public or with another AWS user
users with access can boot the AMI with all the
software + data

15. Cloud Biolinux
The Cloud part
● run Cloud Biolinux on your private cloud ?
● Eucalyptus open source cloud platform
● identical API with EC2, without the usage charges
● easy to set up on your lab's cluster, comes with Ubuntu server (UEC)
● download VMs from Sourceforge ( tinyurl.com/CloudBiolinux-SF )
open.eucalyptus.com

16. Cloud Biolinux
● porting VMs across cloud platforms is not trivial
● Cloud Biolinux VMs from EC2 to Eucalyptus, Xen kernel and boot sector
● framework to share VM configurations ( tinyurl.com/bootstrap-cloudbiolinux )
● based on python-fabric automated deployment tool
● simply edit the software list files and share with collaborators
● they start with fresh VM, python-fabric replicates VM setup on their cloud
tinyurl.com/python-fabric

17. Cloud Biolinux
Collaboration and open source
high-level configuration describing software groups
for each group individual software packages
simply edit the files to change the VM configuration
tinyurl.com/CloudBioLinux-github
...............

18. Cloud Biolinux
The community
● from JCVI and NEBC to an open-source, community-based project
● community initiated during tele-conference meeting at SC '10, Portland, OR
● first meeting past July in Boston, tinyurl.com/openbio-codefest-2010
● work done: 64-bit AMIs, NX remote desktop, set-up the fabric framework
● next year's at ISMB/BOSC in Vienna, Austria http://metalab.at/
● cloudbiolinux.com and most important, tinyurl.com/cloudbiolinux-lists

19. Cloud Biolinux
The future
● expand community, receive feedback, add more software to the VM
● genome assemblers, high-memory EC2 instances up to 68GB RAM
● Hadoop / MapReduce (for those running the VM in private clouds)
● analysis pipelines that are used by large sequencing centers
● actively seeking funding to put major effort in development
● tinyurl.com/cloudbiolinux-lists or community@cloudbiolinux.com

20. Acknowledgments & Credits
Brad Chapman - development of the fabric scripts and community organizer
Tim Booth, Bela Tiwari – BioLinux 6.0 development and EC2 documentation
Deepak Singh and AWS - education grant supporting codefest workshop
Justin Johnson – community and sponsorship of cloudbiolinux.com
J. Craig Venter Inst. - time allowed to work on an open-source project
D. Gomez, E. Navarro, J. Shao, I. Singh – JCVI technology innovation
Members of the Cloud Biolinux community:
Enis Afgan
Michael Heuer
Richard Holland
Mark Jensen Thank you !
Dave Messina
Steffen Möller
Roman Valls