Bionimbus Cambridge Workshop (3-28-11, v7)
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Bionimbus is a cloud-based platform designed for the storage, analysis, and sharing of genomics data, enabling users to manage large data sets efficiently. It operates as both a community cloud and a private cloud, providing various cloud services for data processing and analysis. The platform is part of the Open Science Data Cloud initiative, facilitating collaborations among numerous research institutions and organizations.
Bionimbus Cambridge Workshop (3-28-11, v7)
- 1. Bionimbus: A Cloud-Based Infrastructure for Managing, Analyzing and Sharing Genomics Data March 29, 2011Robert GrossmanInstitute for Genomics & Systems BiologyComputation InstituteUniversity of ChicagoandOpen Cloud Consortium
- 2. Part 1Biology, Big Data & Clouds2Two of the 14 high throughput sequencers at the Ontario Institute for Cancer Research (OICR).
- 4. The Challenge is to Support Cubes of Next Gen Sequence DataEach cell in data cube can be ChIP-chip, ChIP-seq, RNA-seq, movie, etc. data set.Different developmental stagesDifferent pathologiesPerturb the environment
- 5. Genomics as a Big Data Science
- 6. What is a new about clouds?6
- 8. Elastic, On-Demand Computing with Usage Based Pricing Is New8costs the same as1 computer in a rack for 120 hours120 computers in three racks for 1 hour
- 9. Part 2. What is Bionimbus?www.bionimbus.org
- 10. Bionimbus is a community cloud for storing, analyzing and sharing genomics and related data.
- 11. Step 2. Send sample tobe sequenced.Step 1. Get Bionimbus ID (BID), assign project, private/community, public cloud, etc.IGSBSequencersBID GeneratorExternal SequencersStep 5. Cloud based analysis using IGSB and 3rdparty tools and applications. Step 3a. Return rawreads.Step 3b. Returnvariant calls, CNV, annotation…Bionimbus Private Cloud UCBionimbus Community CloudStep 4. Secure datarouting to appropriatecloud based upon BID.Bionimbus Private Cloud XYAmazondbGaP
- 12. What is a good unit to understand data intensive computing of biological data?
- 13. Bionimbus & OSDC TodayThe NIH in the U.S. currently makes available for download approximately 2PB of data.Bionimbus 2010 consists of 6 racks, 212 nodes, 1568 cores and 0.9 PB of storage.Bionimbus is part of the POC Open Science Data Cloud that consists of 14 racks, 472 nodes, 3776 cores and 3+ PB of storage.
- 14. GWT-based Front EndElastic Cloud ServicesDatabase ServicesAnalysis Pipelines & Re-analysis ServicesIntercloud ServicesLarge Data Cloud ServicesData Ingestion Services
- 15. Bionimbus Deployment OptionsBionimbus Community Cloudwww.bionimbus.orgBionimbusAMIs & Amazon hosted applicationsBionimbus Private Clouds
- 16. Part 3. Some Bionimbus Case
- 17. Case Study: Public Datasets in Bionimbus
- 18. Case Study: ModENCODEBionimbus is used to process the modENCODE data from the White lab (over 1000 experiments).BionimbusVMs were used for some of the integrative analysis.Bionimbus is used as a backup for the modENCODE DCC
- 19. Case Study: IGSBAll samples processed by the Institute for Genomics & Systems Biology High-Throughput Genome Analysis Core (HGAC) at the University of Chicago use Bionimbus.
- 20. Bionimbus Virtual Machine Releases 20
- 21. Part 4What is the OSDC?
- 22. Open Science Data CloudAstronomical dataBiological data (Bionimbus)NSF-PIRE OSDC Data ChallengeEarth science data (& disaster relief)
- 23. 23U.S based not-for-profit corporation.
- 24. Manages cloud computing infrastructure to support scientific research: Open Science Data Cloud.
- 25. Manages cloud computing testbeds: Open Cloud Testbed.
- 26. Develop reference implementations, benchmarks and standards.www.opencloudconsortium.org
- 27. OCC MembersCompanies: Cisco, Citrix, Yahoo!, …Universities: University of Chicago, Calit2, Johns Hopkins, Northwestern Univ., ORNL, University of Illinois at Chicago, …Federal agencies: NASAOther: National Lambda RailAdding international partnersin 2011.24
- 28. Infrastructure2010 Proof-of-Concept Infrastructure450+ nodes3000+ cores3+ PBFour data centers (two more to come in 2011)Data centers have 10G network connections (some 100G links in 2011)Plan to add approximately 1 PB of data in 2011.With current funding, we will refresh 1/3 of the infrastructure in 2011 and 2012.
- 29. Towards a Long Term, Sustainable ModelCap Exp about $1M/yearOp Exp about $1M/yearMoore Foundation providing $1M/year for 2011 and 2012 to support the Cap Exp.
- 30. Variety of analysisScientist with laptopWideOpen Science Data CloudMedSequencing centers, LHC, LSSTLowData SizeMedium to Large SmallVery LargeDedicated infrastructureNo infrastructureGeneral infrastructure
- 31. Persistent dataLargedata cloudsMeddatabasesHPCSmallCyclesLarge & spec. clustersSmall to medium clustersSingle workstations
- 32. Bionimbus Team*David Hanley, Nicolas Negre, Elizabeth Bartom, Nicholas Bild, Christopher D. Brown, Marc Domanus, , Robert L Grossman, A. Jason Grundstad, Xiangjun Liu, Michal Sabala, Parantu K Shah, Kevin P WhiteInstitute for Genomics & Systems BiologyUniversity of ChicagoJia Chen, YunhongGu and Damian RoqueiroUniversity of Illinois at ChicagoLincoln Stein and ZhengZhaOntario Institute for Cancer Research*In alphabetical order
- 33. Acknowledgements
- 34. Questions?
- 35. Thank YouFor more information: www.bionimbus.orgwww.opencloudconsortium.orgwww.igsb.orgrgrossman.com