Bionimbus is an open source cloud based system for managing, analyzing and sharing genomic data.

1. An Overview ofBionimbus and the Open Cloud Consortium Robert Grossman Open Cloud Consortium Institute for Genomics & Systems BiologyUniversity of Chicago Laboratory for Advanced ComputingUniversity of Illinois at Chicago

2. Part 1. Bionimbus www.bionimbus.org

3. Web Portal & Widgets Elastic Cloud Services Database Services Analysis Pipelines & Re-analysis Services Scalable data transport Large Data Cloud Services Ingestion Services

4. Case Study 1: Cistrack Resource for cis-regulatory data. Integrates databases and large data clouds. Open source. Contains raw data, intermediate, and analyzed data from approximately 300 experiments from Agilent, Affy and Solexa platforms.

5. Flynet Provides Web2.0 Access to Cistrack

6. Cube is an Elastic Cloud For Re-analysis

7. Case Study 2 ssh modENCODE Worm/Fly peak calling reanalysis Virtual Machines Working Space Simple Persistent Storage (glusterfs) ftp Hypervisers App App App Racks of Hardware OS OS OS Private cloud (Eucalyptus & Cube)

8. Hybrid Clouds ami-efa24c86 Virtual Machines Virtual machine containing (small) data & pipelines Hypervisers App App App Hardware Cluster OS OS OS Public cloud Private / Community cloud

9. Case Study 3 71 rare, deleterious SNP genotypes were validated by Sequenom. SNP concordance: Alignment against gene models: 46% TopHat alignment: 91% Ran TopHat in Bionimbus using VMs and cube. Total time went from 25 days to 1 day.

10. Bionimbus Delivery Mechanisms Login and use the Bionimbus cloud. Use Bionimbus Virtual Machine Images in a) your private cloud; b) Bionimbus cloud; c) public clouds such as Amazon. Bionimbus is open source and you can build your own cloud (and interoperate with ours) (First release of integrated system 3Q 2010) Bionimbus data services for genomic data, even for large datasets

11. Elastic Clouds Large Data Clouds Goal: Minimize cost of virtualized machines & provide on-demand. HPC Goal: Maximize data (with matching compute) and control cost. Goal: Minimize latency and control heat.

12. A successful cloud will… Web 2.0/3.0 user interface Compute services at the scale of a data center. High speed network to move & share the data Persist & refresh data over the long term

13. Part 2. www.opencloudconsortium.org 13

14. 501(c)(3) Not-for-profit corporation Develops standards, interoperability frameworks, and reference implementations. Operates clouds. Develops benchmarks. One area of focus: bridge between private and public clouds. 14 www.opencloudconsortium.org

16. Open Science Data Cloud

17. IntercloudTestbed

19. Open Cloud Consortium Perspective Vendor neutral Open, interoperable architecture Experiment at scale Operate infrastructure at the scale of a small data center Long term point of view (think like a library not cloud service provider) Think public, private & hybrid clouds

20. Condo Clouds Raywulf rack

22. Sector/Sphere

23. Thrift

24. KVM VMs

25. Eucalyptus VMsMREN 19

26. Open Science Data Cloud Astronomical data Biological data (Bionimbus) Networking data Image processing for disaster relief 20

27. Applications Apps Compute Services CloudMetadata Services Data Services PaaS Storage Services Identity Manager Virtual Machine Manager Virtual Network Manager IaaS Network Transport

29. Cloud Compute Services

30. Data/Table Cloud Services

32. Virtual Data Centers (VDC)

33. Virtual Networks (VN)

34. Virtual Machines (VM)Open Cloud Computing Interface (OCCI) Open Virtualization Format (OVF)

35. OCC Benchmarks There are surprises.

36. Acknowledgements

37. Thank You For more information: www.bionimbus.org www.opencloudconsortium.org rgrossman.com (for research papers, etc.)