F06-Cloud-Enabling NGS

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This document summarizes a presentation about CloudMan, a platform for deploying cloud computing resources and Galaxy instances. CloudMan allows users to setup cloud clusters in minutes without expertise, provides over 700GB of reference genomes and bioinformatics tools, and enables customization and sharing of derived cluster instances. It bridges users, isolated Galaxy instances, and cloud infrastructure. Key features include deployment on AWS, automated configuration, dynamic storage, and elastic scaling of resources.

Technology Business

C A M P A I G N
Chief Development Officer
Emory University
C A M P A I G N
School of Nursing Development
Emory University
1520 Clifton Road, NE
School of Nursing Development
Atlanta, Georgia 30322-4207
1520 Clifton Road, NE
P 404.727.1234
Atlanta, Georgia 30322-4207
E adorrill@emory.edu
Discovery of human heteroplasmic sites P 404.727.1234

Enabling of human heteroplasmic sites
enabled NGS analysis with(out)
E adorrill@emory.edu
Discovery by an accessible interface to
cloud computing infrastructure to
enabled by infrastructure
the an accessible interface
cloud computing infrastructure
Enis Afgan, the Galaxy Team,Francesca Chiaromonte
Enis Afgan, Hiroki Goto, Ian Paul,
Anton Nekrutenko,
James Taylor
Kateryna Makova, Anton Nekrutenko, James Taylor
Enis Afgan, Hiroki Goto, Ian Paul, Francesca Chiaromonte
Kateryna Makova, Anton Nekrutenko, James Taylor
Bioinformatics Open Source Conference, July 16, 2011, Vienna

missions: you are free to blog or live-blog about this presentation as long as you attribute the work to its au

CloudMan-as-a-Bridge
A. Users in different labs B. Isolated Galaxy instance(s) C. Dense data center

CloudMan-as-a-Bridge
A. Users in different labs B. Isolated Galaxy instance(s) C. Dense data center

SaaS

CloudMan-as-a-Bridge
A. Users in different labs B. Isolated Galaxy instance(s) C. Dense data center

SaaS IaaS

CloudMan-as-a-Bridge
A. Users in different labs B. Isolated Galaxy instance(s) C. Dense data center

SaaS CloudMan + Galaxy IaaS

CloudMan Platform

A complete solution for instantiating and
managing cloud resources
With automatically conﬁgured Galaxy (if desired)
Scope of tools and reference datasets exceed Galaxy Main

Deploy a (Galaxy) cluster in minutes!

CloudMan features
• Deployment on Amazon Web Services Cloud
• Wizard-guided setup: requires no computational expertise, no
infrastructure, no software
• Automated (thus reproducible) conﬁguration for machine image, tools,
and data
• Four modes of cluster type setup
• Dynamic persistent storage
• Elastic resource scaling: manual or automatic based on workload
• Standalone deployment, requiring no external dependencies or services
• Customizable by individual users
• Sharing of derived cluster instances -> even the customized ones!

CloudBioLinux + Galaxy
+ CloudMan =
• A lot of (NGS) tools immediately available
and easily accessible
• 700GB of reference genome data

Bowtie, BWA, Samtools, MAQ, BFAST, ABySS, Velvet,
MACS, Tophat, Cuﬄinks, MegaBLAST, BLAST, Sputnik,
Taxonomy, HyPhy, Lastz, Perm, GATK, Srma, Beam, Pass,
LPS, Plink, Haploview, Freebayes, Mosaik, Picard, ...

But what if your tool
(or data) is missing?
1. Add it! (via automation)
- CloudMan instances
are self-contained

2. Save & share Add tools
- With individual users
or make it public
Add data

Use CloudMan as SaaS

Use CloudMan as PaaS

It’s automated, reproducible, extensible, and
transparent.

Enis Afgan Dannon Baker Dan Blankenberg Nate Coraor

Dave Clements Jeremy Goecks Jennifer Jackson Greg von Kuster

Kanwei Li James Taylor Kelly Vincent Anton Nekrutenko

Supported by the NHGRI (HG005542, HG004909, HG005133), NSF (DBI-0850103), Penn State University,
Emory University, and the Pennsylvania Department of Public Health

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F06-Cloud-Enabling NGS

1. C A M P A I G N Chief Development Officer Emory University C A M P A I G N School of Nursing Development Emory University 1520 Clifton Road, NE School of Nursing Development Atlanta, Georgia 30322-4207 1520 Clifton Road, NE P 404.727.1234 Atlanta, Georgia 30322-4207 E adorrill@emory.edu Discovery of human heteroplasmic sites P 404.727.1234 Enabling of human heteroplasmic sites enabled NGS analysis with(out) E adorrill@emory.edu Discovery by an accessible interface to cloud computing infrastructure to enabled by infrastructure the an accessible interface cloud computing infrastructure Enis Afgan, the Galaxy Team,Francesca Chiaromonte Enis Afgan, Hiroki Goto, Ian Paul, Anton Nekrutenko, James Taylor Kateryna Makova, Anton Nekrutenko, James Taylor Enis Afgan, Hiroki Goto, Ian Paul, Francesca Chiaromonte Kateryna Makova, Anton Nekrutenko, James Taylor Bioinformatics Open Source Conference, July 16, 2011, Vienna missions: you are free to blog or live-blog about this presentation as long as you attribute the work to its au

2. CloudMan-as-a-Bridge A. Users in different labs B. Isolated Galaxy instance(s) C. Dense data center

3. CloudMan-as-a-Bridge A. Users in different labs B. Isolated Galaxy instance(s) C. Dense data center SaaS

4. CloudMan-as-a-Bridge A. Users in different labs B. Isolated Galaxy instance(s) C. Dense data center SaaS IaaS

5. CloudMan-as-a-Bridge A. Users in different labs B. Isolated Galaxy instance(s) C. Dense data center SaaS CloudMan + Galaxy IaaS

6. CloudMan Platform A complete solution for instantiating and managing cloud resources With automatically conﬁgured Galaxy (if desired) Scope of tools and reference datasets exceed Galaxy Main Deploy a (Galaxy) cluster in minutes!

7. CloudMan features • Deployment on Amazon Web Services Cloud • Wizard-guided setup: requires no computational expertise, no infrastructure, no software • Automated (thus reproducible) conﬁguration for machine image, tools, and data • Four modes of cluster type setup • Dynamic persistent storage • Elastic resource scaling: manual or automatic based on workload • Standalone deployment, requiring no external dependencies or services • Customizable by individual users • Sharing of derived cluster instances -> even the customized ones!

8. CloudMan features • Deployment on Amazon Web Services Cloud • Wizard-guided setup: requires no computational expertise, no infrastructure, no software • Automated (thus reproducible) conﬁguration for machine image, tools, and data • Four modes of cluster type setup • Dynamic persistent storage • Elastic resource scaling: manual or automatic based on workload • Standalone deployment, requiring no external dependencies or services • Customizable by individual users • Sharing of derived cluster instances -> even the customized ones!

9. Deploying a cluster on AWS 1.

10. Deploying a cluster on AWS 1. 2.

11. Deploying a cluster on AWS 1. 2. 3.

12. Deploying a cluster on AWS 1. 2. 3. 4.

13. CloudBioLinux + Galaxy + CloudMan = • A lot of (NGS) tools immediately available and easily accessible • 700GB of reference genome data Bowtie, BWA, Samtools, MAQ, BFAST, ABySS, Velvet, MACS, Tophat, Cuﬄinks, MegaBLAST, BLAST, Sputnik, Taxonomy, HyPhy, Lastz, Perm, GATK, Srma, Beam, Pass, LPS, Plink, Haploview, Freebayes, Mosaik, Picard, ...

14. But what if your tool (or data) is missing? 1. Add it! (via automation) - CloudMan instances are self-contained 2. Save & share Add tools - With individual users or make it public Add data

15. Deployment sharing

16. Deployment sharing

17. Deployment sharing

18. Use CloudMan as SaaS Use CloudMan as PaaS It’s automated, reproducible, extensible, and transparent.

19. Enis Afgan Dannon Baker Dan Blankenberg Nate Coraor Dave Clements Jeremy Goecks Jennifer Jackson Greg von Kuster Kanwei Li James Taylor Kelly Vincent Anton Nekrutenko Supported by the NHGRI (HG005542, HG004909, HG005133), NSF (DBI-0850103), Penn State University, Emory University, and the Pennsylvania Department of Public Health

F06-Cloud-Enabling NGS

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