4-3-12-Genboree_NIH_Cloud_Workshop_demo-kpr

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4-3-12-Genboree_NIH_Cloud_Workshop_demo-kpr
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
• If not, ask or email us ([email protected])
• Genboree.org/microbiome
– Tutorial
– NIH Cloud Workshop Material
– FAQ
• Links also provided on the shared Google doc
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
2
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 NIHNHGRI 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..
Login at www.genboree.org
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
4
Access Microbiome Toolset
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
5
Genboree SNP / Resequencing Toolset
Publications
BMC Genomics (Invited submission)
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
6
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 [email protected]
7
Genboree Epigenomics Toolset
Human Epigenome Atlas and the Genboree Epigenomic 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 [email protected]
8
Launch Genboree Workbench
Hosts / Domains
Groups
Databases
Annotations
Sample sets
Files
Projects
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
9
Managing, Groups, Projects and Databases
Create
Read
Update
Delete
Hosts / Domains
Groups
Databases
Annotations
Sample sets
Files
Projects
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
10
Launch Genboree Workbench
Hosts / Domains
Groups
Databases
Annotations
Sample sets
Files
Projects
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
11
Virtual Data Integration
Genboree Workbenches
www.brainresearch-lab.org
www.microbiomecenter.org
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
www.
genboree.
org
12
Virtual Data Integration
Physical site #1
www.brainresearch-lab.org
Physical site #3
Physical site #2
www.microbiomecenter.org
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
www.
genboree.
org
13
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
Genboree Workbench
UIs
REST API
Executing Tool Job,
Data Storage, Etc
(running in user’s browser)
Compute
Cluster
Person 2
Databases &
File Storage
Person 2
Genboree
Web Site
REST API Server
Servers
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
14
Virtual Data Integration
A combination of dedicated hosting and elastic
cloud computing accessible via the Workbench
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
15
Supplying Credentials to www.microbiome-center.org
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
16
Virtual Integration
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
17
Virtual Integration
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
18
Virtual Integration
Drag and drop
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
19
Virtual Integration
Drag and drop
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
20
Virtual Integration
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
21
Virtual Integration
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
22
Virtual Integration
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
23
Virtual Integration
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
24
Virtual Integration
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
25
Genboree Workbench
Item Details
Data Tree Selector
Data Type
Filter
Input Data
Output
Targets
Various
Data Types
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
26
Genboree Workbench
Activated
Tool
Non-Activated
Tool
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
27
16S Microbiome Toolset Work Flow
1. Setup
2. Transfer
3. Link Samples
to Seq Files
4. Import
Sequences
Create:
•
•
•
•
Sample
Meta Data
Group
Database
Project
Sample
Meta Data
SRR, SFF
Sequences
Sample
Sample
Record
Sample
Record
Record
5. Run Tools:
• RDP
• QIIME
• Alpha
Diversity
• Machine
Learning
Quality
Filtered
Sequences
α β
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
28
16S Microbiome Toolset Tutorial
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
5.
Run Tools
•
•
•
•
RDP – Taxonomic Abundance Pipeline
QIIME Pipeline – OTU Table, Phylogenetic Tree, and Beta Diversity
Alpha Diversity
Aleksandar Milosavljevic, Baylor College of
Machine Learning
Medicine [email protected]
29
16S Microbiome
= end results
= 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
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
Feature Selection
30
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
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
» 7 body sites
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
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
» 7 body sites
32
Introduction to 16S Analysis
• http://www.Genboree.org/microbiome
– http://genboree.org/theCommons/projects/pubgen-microbiome/wiki/Microbiome_Tutorial
• 5 Stool samples
• 5 Throat samples
– Group
• NIH_CLOUD_WORKSHOP
– Database
• nih_workshop_tutorial
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
33
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
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
» 7 body sites
34
Replicating Published Data
• Lean vs obese twin study
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
35
Lean vs. Obese Twins Study
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
36
Lean vs. Obese Twins Study
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
37
Lean vs. Obese Twins Study
• 94 samples
– 49 Lean
– 45 Obese
• V6 primer region
• 454 – 16S rRNA
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
38
Lean vs. Obese Twins Study
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
39
Lean vs. Obese Twins Study
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
40
Lean vs. Obese Twins Study
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
41
Lean vs. Obese Twins Study
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
42
Lean vs. Obese Twins Study
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
43
Lean vs. Obese Twins Study
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
44
Lean vs. Obese Twins Study
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
45
Lean vs. Obese Twins Study
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
46
Lean vs. Obese Twins Study
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
47
Lean vs. Obese Twins Study
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
48
Lean vs. Obese Twins Study
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
49
Lean vs. Obese Twins Study
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
50
Lean vs. Obese Twins Study
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
51
Genboree Project Integration
• http://genboree.org/javabin/project.jsp?projectName=Turnbaugh_lean
_obese_twins_project
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
52
Phylogenetic Visualizations - iTOL
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
53
Lean vs. Obese Twins Study
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
54
Lean vs. Obese Twins Study
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
55
Lean vs. Obese Twins Study
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
56
Lean vs. Obese Twins Study
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
57
Lean vs. Obese Twins Study
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
58
Lean vs. Obese Twins Study
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
59
Lean vs. Obese Twins Study
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
60
Lean vs. Obese Twins Study
Aleksandar Milosavljevic, Baylor College of
[email protected]
457|22 January 2009|
Medicine
61
doi:10.1038/nature07540
Lean vs. Obese Twins Study
Aleksandar Milosavljevic, Baylor College of
MedicineVol
[email protected]
457|22 January
62
2009| doi:10.1038/nature07540
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
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
» 7 body sites
63
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)
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
64
HMP Data Metrics
• Phase I and Phase II
– http://trace.ncbi.nlm.nih.gov/Traces/sra/?study=S
RP002395
– http://trace.ncbi.nlm.nih.gov/Traces/sra/?study=S
RP002860
– > 13,000 samples
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
65
Grid Viewer
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
66
16S rRNA Sample Grid Viewer
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
67
16S rRNA Sample Grid Viewer
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
68
16S rRNA Sample Grid Viewer
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
69
16S rRNA Sample Grid Viewer
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
70
16S rRNA Sample Grid Viewer
• Then show how we can use these sample sets
for analysis on the GMT
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
71
16S rRNA Sample Grid Viewer
•
•
http://genboree.org/javabin/sampleGridViewer.jsp?dbList=http%3A%2F%2Fgenboree.org%2FREST%2Fv1%2
Fgrp%2FHMP-16S-rRNA-phaseI-phaseII%2Fdb%2FHMP-16S-III%3F&gbGridXAttr=primer_region&gbGridYAttr=body_site&xlabel=primer_region
&ylabel=body_site&gridTitle=Samples%20from%20HMP-16S-III&pageTitle=Sample%20Grid%20Viewer:%20Samples%20from%20HMP-16S-I-II
http://genboree.org/javabin/sampleGridViewer.jsp?dbList=http%3A%2F%2Fgenboree.org%2FREST%2Fv1%2
Fgrp%2FHMP-16S-rRNA-phaseI-phaseII%2Fdb%2FHMP-16S-III%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-III&pageTitle=Sample%20Grid%20Viewer:%20Samples%20from%20HMP-16S-I-II
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
72
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
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
» 7 body sites
73
KEGG Mashup
• Genes and Pathways
– View samples + tracks within Grid Viewer
– View output within Gene Browser and Pathway
Browser
– View Pathways within KEGG
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
74
KEGG Mashup
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
75
KEGG Mashup
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
76
KEGG Mashup
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
77
KEGG Mashup
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
78
KEGG Mashup
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
79
KEGG Mashup
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
80
KEGG Mashup
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
81
KEGG Mashup
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
82
KEGG Mashup
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
83
KEGG Mashup
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
84
KEGG Mashup
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
85
KEGG Mashup
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
86
KEGG Mashup
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
87
KEGG Mashup
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
88
KEGG Mashup
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
89
Questions?
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
90
Virtual Integration
• Accessing data that exists within different
physical servers
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
91
Virtual Integration
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
92
Virtual Integration
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
93
Virtual Integration
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
94
Virtual Integration
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
95
Virtual Integration
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
96
Virtual Integration
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
97
Virtual Integration
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
98
Virtual Integration
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
99
Virtual Integration
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
100
Virtual Integration
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
101
Virtual Integration
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
102
Virtual Integration
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
103
Virtual Integration
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
104
Virtual Integration
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
105
Virtual Integration
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
106
•
•
•
•
http://genboree.org/java-bin/sampleGridViewer.jsp?dbList=http%3A%2F%2Fgenboree.org%2FREST%2Fv1%2Fgrp%2FHMP-16S-rRNAphaseI-phaseII%2Fdb%2FHMP-16S-III%3F,http%3A%2F%2Fgenboree.org%2FREST%2Fv1%2Fgrp%2FPublic_16S_experiment_data%2Fdb%2FDisease_X%3F&gbGridXAttr=TY
PE&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-III,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-rRNAphaseI-phaseII%2Fdb%2FHMP-16S-III%3F,http%3A%2F%2Fgenboree.org%2FREST%2Fv1%2Fgrp%2FPublic_16S_experiment_data%2Fdb%2FDisease_X%3F&gbGridXAttr=pri
mer_region&gbGridYAttr=body_site&xlabel=primer_region&ylabel=body_site&gridTitle=Samples%20from%20HMP-16S-III,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-rRNAphaseI-phaseII%2Fdb%2FHMP-16S-III%3F,http%3A%2F%2Fgenboree.org%2FREST%2Fv1%2Fgrp%2FPublic_16S_experiment_data%2Fdb%2FDisease_X%3F&gbGridXAttr=ba
rcode&gbGridYAttr=primer_region_PLUS_body_site&xlabel=barcode&ylabel=primer_region_PLUS_body_site&gridTitle=Samples%20fr
om%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-rRNAphaseI-phaseII%2Fdb%2FHMP-16S-III%3F,http%3A%2F%2Fgenboree.org%2FREST%2Fv1%2Fgrp%2FPublic_16S_experiment_data%2Fdb%2FDisease_X%3F&gbGridXAttr=TY
PE&gbGridYAttr=primer_region_PLUS_body_site&xlabel=TYPE&ylabel=primer_region_PLUS_body_site&gridTitle=Samples%20from%20
HMP-16S-I-II,Disease_X&pageTitle=Sample%20Grid%20Viewer:%20Samples%20from%20HMP-16S-I-II,Disease_X
Aleksandar Milosavljevic, Baylor College of
Medicine [email protected]
107

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