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Genboree Microbiome Toolset and Virtual Data Integration Kevin P. Riehle Matthew E. Roth Aleksandar Milosavljevic Baylor

Genboree Microbiome Toolset and Virtual Data Integration Kevin P. Riehle Matthew E. Roth Aleksandar Milosavljevic Baylor College of Medicine April 2-4, 2012 Boulder, Colorado. Genboree Introduction. Genboree.org Everyone should have received an email regarding their Genboree account

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Genboree Microbiome Toolset and Virtual Data Integration Kevin P. Riehle Matthew E. Roth Aleksandar Milosavljevic Baylor

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  1. Genboree Microbiome Toolset and Virtual Data Integration Kevin P. Riehle Matthew E. Roth AleksandarMilosavljevic Baylor College of Medicine April 2-4, 2012 Boulder, Colorado

  2. Genboree Introduction • Genboree.org • Everyone should have received an email regarding their Genboree account • If not, ask or email us (riehle@bcm.edu) • Genboree.org/microbiome • Tutorial • NIH Cloud Workshop Material • FAQ • Links also provided on the shared Google doc AleksandarMilosavljevic, Baylor College of Medicine amilosav@bcm.edu

  3. References and Acknowledgments Invited to BCM Bioinformatics: Additional contributors not acknowledged in the reference above: R. Alan Harris, Tim Charnecki Funding: This project was supported in part by the NIH Roadmap Epigenomics (Common Fund) U01 DA025956 and NIH-NHGRI R01HG004009 grants to AM, by the NIH-NIDDK UH3 DK083990, P30 DK56338, and NIH Common Fund and NIH-NHGRI U54 HG003273 and U54 HG004973 grants to JV, and by Burroughs Welcome Fund Preterm Birth Initiative and NIH DP21DP2OD001500-01 grants to KA..

  4. Login at www.genboree.org Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  5. Access Microbiome Toolset Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  6. Genboree SNP / Resequencing Toolset • Publications BMC Genomics (Invited submission) Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  7. Genboree RNA Toolset • Publications enabled by the Genboree small RNA Toolset • Gunaratne PH, Lin YC, Benham AL, Drnevich J, Coarfa C, Tennakoon JB, Creighton CJ, Kim JH, Milosavljevic A, Watson M, Griffiths-Jones S, Clayton DF. “Song exposure regulates known and novel microRNAs in the zebra finch auditory forebrain.” BMC Genomics. 2011 May 31;12(1):277. • Shohet JM, Ghosh R, Coarfa C, Ludwig A, Benham AL, Chen Z, Patterson DM, Barbieri E, Mestdagh P, Sikorski DN, Milosavljevic A, Kim ES, Gunaratne PH. “A genome-wide search for promoters that respond to increased MYCN reveals both new oncogenic and tumor suppressor microRNAs associated with aggressive neuroblastoma. “ Cancer Res. 2011 Jun 1;71(11):3841-51. • Buchold GM, Coarfa C, Kim J, Milosavljevic A, Gunaratne PH, Matzuk MM. “Analysis of microRNA expression in the prepubertal testis. “ PLoS One. 2010 Dec 29;5(12):e15317. • Polikepahad S, Knight JM, Naghavi AO, Oplt T, Creighton CJ, Shaw C, Benham AL, Kim J, Soibam B, Harris RA, Coarfa C, Zariff A, Milosavljevic A, Batts LM, Kheradmand F, Gunaratne PH, Corry DB. “Proinflammatory role for let-7 microRNAS in experimental asthma.” J Biol Chem.2010 Sep 24;285(39):30139-49. • Ma L, Buchold GM, Greenbaum MP, Roy A, Burns KH, Zhu H, Han DY, Harris RA, Coarfa C, Gunaratne PH, Yan W, Matzuk MM. “GASZ is essential for male meiosis and suppression of retrotransposon expression in the male germline.” PLoS Genet. 2009 Sep;5(9):e1000635. Epub 2009 Sep 4. Erratum in: PLoS Genet. 2009 Dec;5(12). Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  8. GenboreeEpigenomics Toolset • Human Epigenome Atlas and the GenboreeEpigenomic Toolset for Comparative Epigenome Analysis • Coarfa C1, Harris RA1, Jackson AR1, Pichot CS2, Raghuraman S1, Paithankar S1, Lee AV3, McGuire SE2, Milosavljevic A1 • 1NIH Roadmap Epigenomics Data Analysis and Coordination Center (EDACC), Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas. 2Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas. 3Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania.. • The NIH Roadmap Epigenomics Program Investigators’ Meeting, May 14-15 2012, Bethesda, Maryland, USA. Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  9. Launch Genboree Workbench Hosts / Domains Groups Databases Annotations Sample sets Files Projects Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  10. Managing, Groups, Projects and Databases Create Read Update Delete Hosts / Domains Groups Databases Annotations Sample sets Files Projects Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  11. Launch Genboree Workbench Hosts / Domains Groups Databases Annotations Sample sets Files Projects Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  12. Virtual Data Integration Genboree Workbenches www. genboree. org www.brain-research-lab.org www.microbiome-center.org Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  13. Virtual Data Integration Physical site #3 Physical site #1 Physical site #2 www. genboree. org www.brain-research-lab.org www.microbiome-center.org Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  14. Genboree Workbench UIs (running in user’s browser) REST API Executing Tool Job, Data Storage, Etc Compute Cluster Databases & File Storage Web Site Servers Genboree REST API Server Virtual Data Integration via Genboree REST APIs wwww.genboree.org hosted at Baylor www.brain-research-lab.org and www.microbiome-center.org at Rackspace Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  15. Virtual Data Integration A combination of dedicated hosting and elastic cloud computing accessible via the Workbench Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  16. Supplying Credentials to www.microbiome-center.org Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  17. Virtual Integration Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  18. Virtual Integration Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  19. Virtual Integration Drag and drop Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  20. Virtual Integration Drag and drop Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  21. Virtual Integration Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  22. Virtual Integration Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  23. Virtual Integration Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  24. Virtual Integration Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  25. Virtual Integration Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  26. Genboree Workbench Item Details Data Tree Selector Input Data Data Type Filter Output Targets Various Data Types Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  27. Genboree Workbench Activated Tool Non-Activated Tool Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  28. 16S Microbiome Toolset Work Flow • 5. Run Tools: • RDP • QIIME • Alpha Diversity • Machine Learning 3. Link Samples to Seq Files 4. Import Sequences 1. Setup 2. Transfer • Create: • Sample Meta Data • Group • Database • Project Sample Meta Data Quality Filtered Sequences Sample Record Sample Record Sample Record SRR, SFF Sequences αβ Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  29. 16S Microbiome ToolsetTutorial 1. Setup • Create Sample Meta Data • Create Group • Create Database • Create Project 2. Transfer • Upload Files • View Uploaded Files • Import Samples • View Imported Samples 3. Link Samples to Sequence Files 4. Import Sequences • View Imported Sequences • Analysis • Run Tools • RDP – Taxonomic Abundance Pipeline • QIIME Pipeline – OTU Table, Phylogenetic Tree, and Beta Diversity • Alpha Diversity • Machine Learning Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  30. = end results 16S Microbiome = intermediate result Quality Filtered Sequences Multi-step OTU Picking Taxonomic Classification Remove Chimeras Taxonomic Abundance Representative Sequences OTU Table Phylogenetic Tree Beta Diversity Alpha Diversity Classification Feature Selection Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  31. Microbiome Tutorial 1. Introduction to 16S Analysis • Genboree.org/microbiome • http://genboree.org/theCommons/projects/pub-gen-microbiome/wiki/Microbiome_Tutorial • 5 Stool samples • 5 Throat samples 2. Replicating Published Data • A core gut microbiome in obese and lean twins (Turnbaugh et al, Nature, 2009) • Study objective: To address the question of how host genotype, environmental exposures, and host adiposity influence the gut microbiome • http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2677729/pdf/nihms74182.pdf • 49 Lean Stool samples • 45 Obese Stool samples • Comparing the alpha diversity between lean and obese stool samples 3. Utilizing HMP control data • > 13,000 samples • 18 body sites • 3 primer regions 4. KEGG Mashups • Subset of HMP WGS HUMAnN output • 50 samples • 7 body sites Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  32. Microbiome Tutorial 1. Introduction to 16S Analysis • Genboree.org/microbiome • http://genboree.org/theCommons/projects/pub-gen-microbiome/wiki/Microbiome_Tutorial • 5 Stool samples • 5 Throat samples 2. Replicating Published Data • A core gut microbiome in obese and lean twins (Turnbaugh et al, Nature, 2009) • Study objective: To address the question of how host genotype, environmental exposures, and host adiposity influence the gut microbiome • http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2677729/pdf/nihms74182.pdf • 49 Lean Stool samples • 45 Obese Stool samples • Comparing the alpha diversity between lean and obese stool samples 3. Utilizing HMP control data • > 13,000 samples • 18 body sites • 3 primer regions 4. KEGG Mashups • Subset of HMP WGS HUMAnN output • 50 samples • 7 body sites Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  33. Introduction to 16S Analysis • http://www.Genboree.org/microbiome • http://genboree.org/theCommons/projects/pub-gen-microbiome/wiki/Microbiome_Tutorial • 5 Stool samples • 5 Throat samples • Group • NIH_CLOUD_WORKSHOP • Database • nih_workshop_tutorial Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  34. Microbiome Tutorial 1. Introduction to 16S Analysis • Genboree.org/microbiome • http://genboree.org/theCommons/projects/pub-gen-microbiome/wiki/Microbiome_Tutorial • 5 Stool samples • 5 Throat samples 2. Replicating Published Data • A core gut microbiome in obese and lean twins (Turnbaugh et al, Nature, 2009) • Study objective: To address the question of how host genotype, environmental exposures, and host adiposity influence the gut microbiome • http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2677729/pdf/nihms74182.pdf • 49 Lean Stool samples • 45 Obese Stool samples • Comparing the alpha diversity between lean and obese stool samples 3. Utilizing HMP control data • > 13,000 samples • 18 body sites • 3 primer regions 4. KEGG Mashups • Subset of HMP WGS HUMAnN output • 50 samples • 7 body sites Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  35. Replicating Published Data • Lean vs obese twin study Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  36. Lean vs. Obese Twins Study Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  37. Lean vs. Obese Twins Study Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  38. Lean vs. Obese Twins Study • 94 samples • 49 Lean • 45 Obese • V6 primer region • 454 – 16S rRNA Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  39. Lean vs. Obese Twins Study Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  40. Lean vs. Obese Twins Study Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  41. Lean vs. Obese Twins Study Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  42. Lean vs. Obese Twins Study Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  43. Lean vs. Obese Twins Study Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  44. Lean vs. Obese Twins Study Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  45. Lean vs. Obese Twins Study Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  46. Lean vs. Obese Twins Study Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  47. Lean vs. Obese Twins Study Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  48. Lean vs. Obese Twins Study Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  49. Lean vs. Obese Twins Study Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

  50. Lean vs. Obese Twins Study Aleksandar Milosavljevic, Baylor College of Medicine amilosav@bcm.edu

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