genboree microbiome toolset

82
Genboree Microbiome Toolset Kevin Riehle 4/3/12 – NIH Cloud Workshop Boulder, Colorado

Upload: shona

Post on 22-Feb-2016

67 views

Category:

Documents


0 download

DESCRIPTION

Genboree Microbiome Toolset. 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 - PowerPoint PPT Presentation

TRANSCRIPT

Page 1: Genboree Microbiome Toolset

Genboree Microbiome Toolset

Kevin Riehle

4/3/12 – NIH Cloud WorkshopBoulder, Colorado

Page 2: Genboree Microbiome Toolset

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

Page 3: Genboree Microbiome Toolset

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

Page 4: Genboree Microbiome Toolset

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.

Page 5: Genboree Microbiome Toolset

Large Scale Applications

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

Page 6: Genboree Microbiome Toolset

Genboree Introduction

• Groups• Permissions• Databases• Projects• Browser• Workbench

Page 7: Genboree Microbiome Toolset

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.

Page 8: Genboree Microbiome Toolset

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

Page 9: Genboree Microbiome Toolset

Data Tree Selector

Genboree Workbench

Various Data Types

Item Details

Data Type Filter

Input Data

Output Targets

Page 10: Genboree Microbiome Toolset

Activated Tool

Non-Activated Tool

Genboree Workbench

Page 11: Genboree Microbiome Toolset

Workbench FlowTransfer Associate Initialize Analyze

SRR, SFF Sequences

Subject Meta Data

Sample Record

Sample Record

Sample Record

Quality FilteredSample Sequences

Samples

SampleSet

α β

Page 12: Genboree Microbiome Toolset

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)

Page 13: Genboree Microbiome Toolset

Data + Tools

• Lean vs obese twin study

Page 14: Genboree Microbiome Toolset

Lean vs. Obese Twins Study

Page 15: Genboree Microbiome Toolset

Lean vs. Obese Twins Study

Page 16: Genboree Microbiome Toolset

Lean vs. Obese Twins Study

• 94 samples– 49 Lean– 45 Obese

• V6 primer region• 454 – 16S rRNA

Page 17: Genboree Microbiome Toolset

Lean vs. Obese Twins Study

Page 18: Genboree Microbiome Toolset

Lean vs. Obese Twins Study

Page 19: Genboree Microbiome Toolset

Lean vs. Obese Twins Study

Page 20: Genboree Microbiome Toolset

Lean vs. Obese Twins Study

Page 21: Genboree Microbiome Toolset

Lean vs. Obese Twins Study

Page 22: Genboree Microbiome Toolset

Lean vs. Obese Twins Study

Page 23: Genboree Microbiome Toolset

Lean vs. Obese Twins Study

Page 24: Genboree Microbiome Toolset

Lean vs. Obese Twins Study

Page 25: Genboree Microbiome Toolset

Lean vs. Obese Twins Study

Page 26: Genboree Microbiome Toolset

Lean vs. Obese Twins Study

Page 27: Genboree Microbiome Toolset

Lean vs. Obese Twins Study

Page 28: Genboree Microbiome Toolset

Lean vs. Obese Twins Study

Page 29: Genboree Microbiome Toolset

Lean vs. Obese Twins Study

Page 31: Genboree Microbiome Toolset

Phylogenetic Visualizations - iTOL

Page 32: Genboree Microbiome Toolset

Lean vs. Obese Twins Study

Page 33: Genboree Microbiome Toolset

Lean vs. Obese Twins Study

Page 34: Genboree Microbiome Toolset

Lean vs. Obese Twins Study

Page 35: Genboree Microbiome Toolset

Lean vs. Obese Twins Study

Page 36: Genboree Microbiome Toolset

Lean vs. Obese Twins Study

Page 37: Genboree Microbiome Toolset

Lean vs. Obese Twins Study

Page 38: Genboree Microbiome Toolset

Lean vs. Obese Twins Study

Page 39: Genboree Microbiome Toolset

Lean vs. Obese Twins Study

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

Page 40: Genboree Microbiome Toolset

Lean vs. Obese Twins Study

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

Page 41: Genboree Microbiome Toolset

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)

Page 42: Genboree Microbiome Toolset

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

Page 43: Genboree Microbiome Toolset

Grid Viewer

Page 44: Genboree Microbiome Toolset

16S rRNA Sample Grid Viewer

Page 45: Genboree Microbiome Toolset

16S rRNA Sample Grid Viewer

Page 46: Genboree Microbiome Toolset

16S rRNA Sample Grid Viewer

Page 47: Genboree Microbiome Toolset

16S rRNA Sample Grid Viewer

Page 48: Genboree Microbiome Toolset

16S rRNA Sample Grid Viewer

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

Page 49: Genboree Microbiome Toolset

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

Page 50: Genboree Microbiome Toolset

Data + Mashup

• Genes and Pathways– View samples + tracks within Grid Viewer– View output within Gene Browser and Pathway

Browser– View Pathways within KEGG

Page 51: Genboree Microbiome Toolset

Data + Mashup

Page 52: Genboree Microbiome Toolset

Data + Mashup

Page 53: Genboree Microbiome Toolset

Data + Mashup

Page 54: Genboree Microbiome Toolset

Data + Mashup

Page 55: Genboree Microbiome Toolset

Data + Mashup

Page 56: Genboree Microbiome Toolset

Data + Mashup

Page 57: Genboree Microbiome Toolset

Data + Mashup

Page 58: Genboree Microbiome Toolset

Data + Mashup

Page 59: Genboree Microbiome Toolset

Data + Mashup

Page 60: Genboree Microbiome Toolset

Data + Mashup

Page 61: Genboree Microbiome Toolset

Data + Mashup

Page 62: Genboree Microbiome Toolset

Data + Mashup

Page 63: Genboree Microbiome Toolset

Data + Mashup

Page 64: Genboree Microbiome Toolset

Data + Mashup

Page 65: Genboree Microbiome Toolset

Data + Mashup

Page 66: Genboree Microbiome Toolset

Virtual Integration

• Accessing data that exists within different physical servers

Page 67: Genboree Microbiome Toolset

Virtual Integration

Page 68: Genboree Microbiome Toolset

Virtual Integration

Page 69: Genboree Microbiome Toolset

Virtual Integration

Page 70: Genboree Microbiome Toolset

Virtual Integration

Page 71: Genboree Microbiome Toolset

Virtual Integration

Page 72: Genboree Microbiome Toolset

Virtual Integration

Page 73: Genboree Microbiome Toolset

Virtual Integration

Page 74: Genboree Microbiome Toolset

Virtual Integration

Page 75: Genboree Microbiome Toolset

Virtual Integration

Page 76: Genboree Microbiome Toolset

Virtual Integration

Page 77: Genboree Microbiome Toolset

Virtual Integration

Page 78: Genboree Microbiome Toolset

Virtual Integration

Page 79: Genboree Microbiome Toolset

Virtual Integration

Page 80: Genboree Microbiome Toolset

Virtual Integration

Page 81: Genboree Microbiome Toolset

Virtual Integration

Page 82: Genboree Microbiome Toolset

• 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