Genboree Microbiome Toolset

1. Genboree Microbiome Toolset 4/3/12 – NIH Cloud Workshop Boulder, Colorado Kevin Riehle

2. Collaborators • Aleks Milosavljevic • Cristi Coarfa • Andrew Jackson • Arpit Tandon • Sameer Paithankar • Sriram Raghuraman Aagaard Lab • Kjersti Aagaard • Jun Ma • Versalovic Lab • James Versalovic • Emily B. Hollister • Delphine Saulnier • Toni-Ann Mistretta • Sabeen Raza Matt Roth Aleksandar Milosavljevic Sabeen Raza James Veralovic Toni-Ann Mistretta Kevin Riehle Jun Ma Delphine Saulnier Emily B. Hollister Kjersti Aagaard Arpit Tandon Sriram Raghuraman Cristi Coarfa Andrew Jackson Sameer Paithankar

3. Overview • Genboree Introduction • Manuscripts • Overview • Data + Tools • Lean vs. obese twins study • Grid viewer + 16S Samples • Data + Mashups • Grid viewer + WGS Genes / Pathways + KEGG • Virtual Integration • Multiple databases existing within multiple servers in different physical locations • Conclusions

4. Genboree Microbiome Toolset Riehle K, Coarfa C, Jackson A, Ma J, Tandon A, Paithankar S, Raghuraman S, Mistretta TA, Saulnier D, Raza S, Diaz MA, Shulman R, Aagaard K, Versalovic J, Milosavljevic A. The genboree microbiome toolset and the analysis of 16S rRNA microbial sequences. BMC Bioinformatics 2012; In Press.

5. Large Scale Applications • Metagenomic-Based Approach to a Comprehensive Characterization of the Vaginal Microbiome Signature in Pregnancy • Kjersti Aagaard, in review

6. Genboree Introduction • Groups • Permissions • Databases • Projects • Browser • Workbench

7. Genboree Introduction • Genboree.org • Everyone should have received an email regarding their Genboree account • Genboree.org/microbiome • Tutorial • FAQ • This PointPoint • Etc. • Questions: • Ask later, interrupt now, etc.

8. 16S rRNA SFF / SRA Sample Meta Data 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

9. Genboree Workbench Item Details Data Tree Selector Input Data Data Type Filter Output Targets Various Data Types

10. Genboree Workbench Activated Tool Non-Activated Tool

11. Workbench Flow Transfer Associate Initialize Analyze Quality Filtered Sample Sequences SRR, SFF Sequences αβ Sample Record Sample Record Sample Record Subject Meta Data Sample Set Samples

12. Samples • Import Samples • If sample does not exist, create • If sample exists • Add metadata if metadata does not exist • Update metadata if metadata exists and differs • Sample – File Linker • Add Sample Set • Delete Sample Set(s) • Add Samples to Sample Set • Remove Samples from Sample Set(s)

13. Data + Tools • Lean vs obese twin study

14. Lean vs. Obese Twins Study

15. Lean vs. Obese Twins Study

16. Lean vs. Obese Twins Study • 94 samples • 49 Lean • 45 Obese • V6 primer region • 454 – 16S rRNA

17. Lean vs. Obese Twins Study

18. Lean vs. Obese Twins Study

19. Lean vs. Obese Twins Study

20. Lean vs. Obese Twins Study

21. Lean vs. Obese Twins Study

22. Lean vs. Obese Twins Study

23. Lean vs. Obese Twins Study

24. Lean vs. Obese Twins Study

25. Lean vs. Obese Twins Study

26. Lean vs. Obese Twins Study

27. Lean vs. Obese Twins Study

28. Lean vs. Obese Twins Study

29. Lean vs. Obese Twins Study

30. Genboree Project Integration • http://genboree.org/java-bin/project.jsp?projectName=Turnbaugh_lean_obese_twins_project

31. Phylogenetic Visualizations - iTOL

32. Lean vs. Obese Twins Study

33. Lean vs. Obese Twins Study

34. Lean vs. Obese Twins Study

35. Lean vs. Obese Twins Study

36. Lean vs. Obese Twins Study

37. Lean vs. Obese Twins Study

38. Lean vs. Obese Twins Study

39. Lean vs. Obese Twins Study Vol 457|22 January 2009| doi:10.1038/nature07540

40. Lean vs. Obese Twins Study Vol 457|22 January 2009| doi:10.1038/nature07540

41. Grid Viewer • Provides an interactive view of Samples from 1 to many databases • Databases may exist in different physical locations (virtual integration) (will discuss more later) • Users can save Sample Sets in which to analyze • Users can select Samples in which to explore Genes and Pathways (WGS only)

42. HMP Data Metrics • Phase I and Phase II • http://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP002395 • http://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP002860 • > 13,000 samples

43. Grid Viewer

44. 16S rRNA Sample Grid Viewer

45. 16S rRNA Sample Grid Viewer

46. 16S rRNA Sample Grid Viewer

47. 16S rRNA Sample Grid Viewer

48. 16S rRNA Sample Grid Viewer • Then show how we can use these sample sets for analysis on the GMT

49. 16S rRNA Sample Grid Viewer • http://genboree.org/java-bin/sampleGridViewer.jsp?dbList=http%3A%2F%2Fgenboree.org%2FREST%2Fv1%2Fgrp%2FHMP-16S-rRNA-phaseI-phaseII%2Fdb%2FHMP-16S-I-II%3F&gbGridXAttr=primer_region&gbGridYAttr=body_site&xlabel=primer_region&ylabel=body_site&gridTitle=Samples%20from%20HMP-16S-I-II&pageTitle=Sample%20Grid%20Viewer:%20Samples%20from%20HMP-16S-I-II • http://genboree.org/java-bin/sampleGridViewer.jsp?dbList=http%3A%2F%2Fgenboree.org%2FREST%2Fv1%2Fgrp%2FHMP-16S-rRNA-phaseI-phaseII%2Fdb%2FHMP-16S-I-II%3F&gbGridXAttr=seq_center&gbGridYAttr=primer_region_PLUS_body_site&xlabel=seq_center&ylabel=primer_region_PLUS_body_site&gridTitle=Samples%20from%20HMP-16S-I-II&pageTitle=Sample%20Grid%20Viewer:%20Samples%20from%20HMP-16S-I-II

50. Data + Mashup • Genes and Pathways • View samples + tracks within Grid Viewer • View output within Gene Browser and Pathway Browser • View Pathways within KEGG