genboree microbiome toolset

Genboree Microbiome Toolset

Kevin Riehle

4/3/12 – NIH Cloud WorkshopBoulder, 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-AnnMistretta

Cristi Coarfa

Kjersti Aagaard

Aleksandar Milosavljevic

Jun Ma

Andrew Jackson Sameer

Paithankar

Emily B. Hollister

Delphine Saulnier

SriramRaghuraman

Arpit Tandon

MattRoth

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 ToolsetRiehle 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 email regarding their

Genboree account• Genboree.org/microbiome– Tutorial– FAQ– This PointPoint– Etc.

• Questions:– Ask later, interrupt now, etc.

16S rRNA SFF / SRA Sample Meta Data

Quality Filtered Sequences

Multi-step OTU Picking

Remove Chimeras

Taxonomic Classification

Representative Sequences

OTU Table Phylogenetic 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 FlowTransfer Associate Initialize Analyze

SRR, SFF Sequences

Subject Meta Data

Sample Record

Sample Record

Sample Record

Quality FilteredSample Sequences

Samples

SampleSet

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

Lean vs. Obese Twins Study

Lean vs. Obese Twins Study

• 94 samples– 49 Lean– 45 Obese

• V6 primer region• 454 – 16S rRNA

Lean vs. Obese Twins Study

Lean vs. Obese Twins Study

Lean vs. Obese Twins Study

Lean vs. Obese Twins Study

Lean vs. Obese Twins Study

Lean vs. Obese Twins Study

Lean vs. Obese Twins Study

Lean vs. Obese Twins Study

Lean vs. Obese Twins Study

Lean vs. Obese Twins Study

Lean vs. Obese Twins Study

Lean vs. Obese Twins Study

Lean vs. Obese Twins Study

Genboree Project Integration

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

Phylogenetic Visualizations - iTOL

Lean vs. Obese Twins Study

Lean vs. Obese Twins Study

Lean vs. Obese Twins Study

Lean vs. Obese Twins Study

Lean vs. Obese Twins Study

Lean vs. Obese Twins Study

Lean vs. Obese Twins Study

Lean vs. Obese Twins Study

Vol 457|22 January 2009| doi:10.1038/nature07540

Lean vs. Obese Twins Study

Vol 457|22 January 2009| doi:10.1038/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– http://trace.ncbi.nlm.nih.gov/Traces/sra/?

study=SRP002395– http://trace.ncbi.nlm.nih.gov/Traces/sra/?study=S

RP002860– > 13,000 samples

Grid Viewer

16S rRNA Sample Grid Viewer

16S rRNA Sample Grid Viewer

16S rRNA Sample Grid Viewer

16S rRNA Sample 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• 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

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

Data + Mashup

Data + Mashup

Data + Mashup

Data + Mashup

Data + Mashup

Data + Mashup

Data + Mashup

Data + Mashup

Data + Mashup

Data + Mashup

Data + Mashup

Data + Mashup

Data + Mashup

Data + Mashup

Virtual Integration

• Accessing data that exists within different physical servers

Virtual Integration

Virtual Integration

Virtual Integration

Virtual Integration

Virtual Integration

Virtual Integration

Virtual Integration

Virtual Integration

Virtual Integration

Virtual Integration

Virtual Integration

Virtual Integration

Virtual Integration

Virtual Integration

Virtual Integration

• 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,http%3A%2F%2Fgenboree.org%2FREST%2Fv1%2Fgrp%2FPublic_16S_experiment_data%2Fdb%2FDisease_X%3F&gbGridXAttr=TYPE&gbGridYAttr=DNA_extraction_site_PLUS_seq_center_PLUS_body_site_PLUS_primer_region&xlabel=TYPE&ylabel=DNA_extraction_site_PLUS_seq_center_PLUS_body_site_PLUS_primer_region&gridTitle=Samples%20from%20HMP-16S-I-II,Disease_X&pageTitle=Sample%20Grid%20Viewer:%20Samples%20from%20HMP-16S-I-II,Disease_X

• 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,http%3A%2F%2Fgenboree.org%2FREST%2Fv1%2Fgrp%2FPublic_16S_experiment_data%2Fdb%2FDisease_X%3F&gbGridXAttr=primer_region&gbGridYAttr=body_site&xlabel=primer_region&ylabel=body_site&gridTitle=Samples%20from%20HMP-16S-I-II,Disease_X&pageTitle=Sample%20Grid%20Viewer:%20Samples%20from%20HMP-16S-I-II,Disease_X

• 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,http%3A%2F%2Fgenboree.org%2FREST%2Fv1%2Fgrp%2FPublic_16S_experiment_data%2Fdb%2FDisease_X%3F&gbGridXAttr=barcode&gbGridYAttr=primer_region_PLUS_body_site&xlabel=barcode&ylabel=primer_region_PLUS_body_site&gridTitle=Samples%20from%20HMP-16S-I-II,Disease_X&pageTitle=Sample%20Grid%20Viewer:%20Samples%20from%20HMP-16S-I-II,Disease_X

• 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,http%3A%2F%2Fgenboree.org%2FREST%2Fv1%2Fgrp%2FPublic_16S_experiment_data%2Fdb%2FDisease_X%3F&gbGridXAttr=TYPE&gbGridYAttr=primer_region_PLUS_body_site&xlabel=TYPE&ylabel=primer_region_PLUS_body_site&gridTitle=Samples%20from%20HMP-16S-I-II,Disease_X&pageTitle=Sample%20Grid%20Viewer:%20Samples%20from%20HMP-16S-I-II,Disease_X