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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.

Published in: Technology

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  • 1. An Overview of Bionimbus 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
    Data 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 Web 2.0 Access to Cistrack
  • 6. Cube is an Elastic Cloud For Re-analysis
  • 7. Case Study 2
    71 rare, deleterious SNP genotypes were validated by Sequenom.
    SNP concordance:
    Alignment against gene models:
    46%
    TopHat alignment:
    91%
    Ran TopHat in Bionimbus using Cube-based VMs.
    Total time went from 25 days to 1 day.
  • 8. Case Study 3
    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)
  • 9. Hybrid Clouds
    ami-efa24c86
    Virtual Machines
    Bionimbus virtual machine images
    Hypervisers
    App
    App
    App
    Hardware Cluster
    OS
    OS
    OS
    Public cloud
    Private / Community cloud
  • 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
  • 15. Operates Clouds
    500 nodes
    3000 cores
    1.5+ PB
    Four data centers
    10 Gbps
    Target to refresh 1/3 each year.
    • Open Cloud Testbed
    • 16. Open Science Data Cloud
    • 17. Cloud-based Disaster Relief Services
  • OCC Members
    Companies: Yahoo, Cisco, Aerospace Corp., Booz Allen Hamilton, InfoBlox, Open Data Group, Raytheon
    Universities: CalIT2, Johns Hopkins, Northwestern University, University of Chicago, University of Illinois at Chicago
    Government agencies: NASA
    16
  • 18. 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
  • 19. Condo Clouds
    Raywulf rack
  • 20. Open Cloud Testbed
    C-Wave
    CENIC
    Dragon
    Phase 2
    9 racks
    250+ Nodes
    1000+ Cores
    10+ Gb/s
    MREN
    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
  • 28. Standards
    • Platform as a Service
    • 29. Cloud Compute Services
    • 30. Data/Table Cloud Services
    • 31. Cloud Storage Services
    Large Data Cloud Interoperability Framework
    SNIA Cloud Data Management Interface (CDMI)
    • Infrastructure as a Service
    • 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.)