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

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

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

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.

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

Genboree Introduction Groups Permissions Databases Projects Browser Workbench

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

16S rRNA SFF / SRASample Meta Data Quality Filtered Sequences Multi-step OTU Picking Remove Chimeras Taxonomic Classification Representative Sequences OTU TablePhylogenetic Tree Beta Diversity Alpha Diversity Classification Feature Selection Taxonomic Abundance

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

Activated Tool Non-Activated Tool Genboree Workbench

Workbench Flow TransferAssociateInitializeAnalyze SRR, SFF Sequences Subject Meta Data Sample Record Quality Filtered Sample Sequences Quality Filtered Sample Sequences Samples Sample Set α β

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)

Data + Tools Lean vs obese twin study

Lean vs. Obese Twins Study

94 samples – 49 Lean – 45 Obese V6 primer region 454 – 16S rRNA

Lean vs. Obese Twins Study

Genboree Project Integration bin/project.jsp?projectName=Turnbaugh_lean _obese_twins_project bin/project.jsp?projectName=Turnbaugh_lean _obese_twins_project

Phylogenetic Visualizations - iTOL

Lean vs. Obese Twins Study

Vol 457|22 January 2009| doi: /nature07540

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

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)

HMP Data Metrics Phase I and Phase II – RP RP – RP RP – > 13,000 samples

Grid Viewer

16S rRNA Sample Grid Viewer

Then show how we can use these sample sets for analysis on the GMT

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

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

Data + Mashup

Virtual Integration Accessing data that exists within different physical servers

Virtual Integration

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