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An Overview of Bionimbus (March 2010)
An Overview of Bionimbus (March 2010)
An Overview of Bionimbus (March 2010)
An Overview of Bionimbus (March 2010)
An Overview of Bionimbus (March 2010)
An Overview of Bionimbus (March 2010)
An Overview of Bionimbus (March 2010)
An Overview of Bionimbus (March 2010)
An Overview of Bionimbus (March 2010)
An Overview of Bionimbus (March 2010)
An Overview of Bionimbus (March 2010)
An Overview of Bionimbus (March 2010)
An Overview of Bionimbus (March 2010)
An Overview of Bionimbus (March 2010)
An Overview of Bionimbus (March 2010)
An Overview of Bionimbus (March 2010)
An Overview of Bionimbus (March 2010)
An Overview of Bionimbus (March 2010)
An Overview of Bionimbus (March 2010)
An Overview of Bionimbus (March 2010)
An Overview of Bionimbus (March 2010)
An Overview of Bionimbus (March 2010)
An Overview of Bionimbus (March 2010)
An Overview of Bionimbus (March 2010)
An Overview of Bionimbus (March 2010)
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An Overview of Bionimbus (March 2010)

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This is a talk I gave at NHGRI in March 2010.

This is a talk I gave at NHGRI in March 2010.

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  • 1. An Overview of Bionimbus and the Open Cloud Consortium<br />Robert Grossman<br />Open Cloud Consortium <br />Institute for Genomics & Systems BiologyUniversity of Chicago<br />Laboratory for Advanced ComputingUniversity of Illinois at Chicago<br />
  • 2. Part 1. Bionimbus<br />www.bionimbus.org<br />
  • 3. Web Portal & Widgets<br />Elastic Cloud Services<br />Database Services<br />Analysis Pipelines & Re-analysis Services<br />Scalable data transport<br />Large Data Cloud Services<br />Data Ingestion Services<br />
  • 4. Case Study 1: Cistrack<br />Resource for cis-regulatory data.<br />Integrates databases and large data clouds.<br />Open source.<br />Contains raw data, intermediate, and analyzed data from approximately 300 experiments from Agilent, Affy and Solexa platforms.<br />
  • 5. Flynet Provides Web 2.0 Access to Cistrack<br />
  • 6. Cube is an Elastic Cloud For Re-analysis<br />
  • 7. Case Study 2<br />71 rare, deleterious SNP genotypes were validated by Sequenom.<br />SNP concordance:<br />Alignment against gene models: <br />46%<br />TopHat alignment: <br />91%<br />Ran TopHat in Bionimbus using Cube-based VMs.<br />Total time went from 25 days to 1 day.<br />
  • 8. Case Study 3<br />ssh<br />modENCODE Worm/Fly peak calling reanalysis<br />Virtual Machines<br />Working Space<br />Simple Persistent Storage (glusterfs)<br />ftp<br />Hypervisers<br />App<br />App<br />App<br />Racks of Hardware<br />OS<br />OS<br />OS<br />Private cloud (Eucalyptus & Cube)<br />
  • 9. Hybrid Clouds<br />ami-efa24c86<br />Virtual Machines<br />Bionimbus virtual machine images <br />Hypervisers<br />App<br />App<br />App<br />Hardware Cluster<br />OS<br />OS<br />OS<br />Public cloud<br />Private / Community cloud<br />
  • 10. Bionimbus Delivery Mechanisms<br />Login and use the Bionimbus cloud.<br />Use Bionimbus Virtual Machine Images in a) your private cloud; b) Bionimbus cloud; c) public clouds such as Amazon.<br />Bionimbus is open source and you can build your own cloud (and interoperate with ours) (First release of integrated system 3Q 2010)<br />Bionimbus data services for genomic data, even for large datasets <br />
  • 11. Elastic Clouds<br />Large Data Clouds<br />Goal: Minimize cost of virtualized machines & provide on-demand. <br />HPC<br />Goal: Maximize data (with matching compute) and control cost.<br />Goal: Minimize latency and control heat.<br />
  • 12. A successful cloud will…<br />Web 2.0/3.0 user interface<br />Compute services at the scale of a data center.<br />High speed network to move & share the data<br />Persist & refresh data over the long term<br />
  • 13. Part 2. <br />www.opencloudconsortium.org<br />13<br />
  • 14. 501(c)(3) Not-for-profit corporation<br />Develops standards, interoperability frameworks, and reference implementations.<br />Operates clouds.<br />Develops benchmarks.<br />One area of focus: bridge between private and public clouds.<br />14<br />www.opencloudconsortium.org<br />
  • 15. Operates Clouds<br />500 nodes<br />3000 cores<br />1.5+ PB<br />Four data centers<br />10 Gbps<br />Target to refresh 1/3 each year.<br /><ul><li>Open Cloud Testbed
  • 16. Open Science Data Cloud
  • 17. Cloud-based Disaster Relief Services</li></li></ul><li>OCC Members<br />Companies: Yahoo, Cisco, Aerospace Corp., Booz Allen Hamilton, InfoBlox, Open Data Group, Raytheon <br />Universities: CalIT2, Johns Hopkins, Northwestern University, University of Chicago, University of Illinois at Chicago<br />Government agencies: NASA<br />16<br />
  • 18. Open Cloud Consortium Perspective<br />Vendor neutral<br />Open, interoperable architecture<br />Experiment at scale<br />Operate infrastructure at the scale of a small data center<br />Long term point of view (think like a library not cloud service provider)<br />Think public, private & hybrid clouds<br />
  • 19. Condo Clouds<br />Raywulf rack<br />
  • 20. Open Cloud Testbed<br />C-Wave<br />CENIC<br />Dragon<br />Phase 2<br />9 racks<br />250+ Nodes<br />1000+ Cores<br />10+ Gb/s <br /><ul><li>Hadoop
  • 21. Sector/Sphere
  • 22. Thrift
  • 23. KVM VMs
  • 24. Eucalyptus
  • 25. Nova</li></ul>MREN<br />19<br />
  • 26. Open Science Data Cloud<br />Astronomical data<br />Biological data (Bionimbus)<br />Networking data<br />Image processing for disaster relief<br />20<br />
  • 27. Applications<br />Apps<br />Compute Services<br />CloudMetadata Services<br />Data Services<br />PaaS<br />Storage Services<br />Identity Manager<br />Virtual Machine Manager<br />Virtual Network Manager<br />IaaS<br />Network Transport<br />
  • 28. Standards<br /><ul><li>Platform as a Service
  • 29. Cloud Compute Services
  • 30. Data/Table Cloud Services
  • 31. Cloud Storage Services</li></ul>Large Data Cloud Interoperability Framework<br />SNIA Cloud Data Management Interface (CDMI)<br /><ul><li>Infrastructure as a Service
  • 32. Virtual Data Centers (VDC)
  • 33. Virtual Networks (VN)
  • 34. Virtual Machines (VM)</li></ul>Open Cloud Computing Interface (OCCI)<br />Open Virtualization Format (OVF)<br />
  • 35. OCC Benchmarks<br />There are surprises.<br />
  • 36. Acknowledgements<br />
  • 37. Thank You<br />For more information:<br />www.bionimbus.org<br />www.opencloudconsortium.org<br />rgrossman.com (for research papers, etc.)<br />

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