Genomics on the Half Shell: Making Science more Open
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Genomics on the Half Shell: Making Science more Open
Steven B. RobertsAssociate Professor
School of Aquatic and Fishery SciencesUniversity of Washington
robertslab.info
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Open Science
•You are free to Share!
•Our lab practices open notebookscience
•Slides and more available @
oystergen.es/data
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Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...
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Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...
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disease resistance
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disease resistance
TranscriptomeProteomeDNA Methylation
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disease resistance
Elevated pCO2 causes developmental delay in early larval Pacific oysters, Crassostrea gigas.Timmins-Schiffman et al 2012
Ocean Acidification
Biology
Environment
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disease resistance
Ocean Acidification
Biology
EnvironmentShotgun Proteomics
10.1093/conphys/cot009
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disease resistance
Ocean Acidification
Shotgun ProteomicsBiology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...eagle.fish.washington.edu/emma
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disease resistance
TranscriptomeProteomeDNA Methylation
Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...
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Function?
Biology
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Molecular
Data Analysis
eScience
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Notebooks
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Platforms
Open Science
Data
everything else...
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mosaic
associated with gene bodies
Photo credit: Flickr, Creative Commons, dkeats
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HiSeq - lane - 70G mapping - 60G
table
Biology
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Molecular
Data Analysis
eScience
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Notebooks
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Open Science
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everything else...
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Stochastic Variation
10.1093/bfgp/elt05410.6084/m9.figshare.880763
Biology
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Molecular
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eScience
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Open Science
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everything else...
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Biology
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Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
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Platforms
Open Science
Data
everything else...
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Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...
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raw - 70G mapping - 60G tables - 40G ........
Biology
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eScience
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everything else...
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Genome
Primary Data Table Groupings
Expressed Sequence Tags
Gene Expression Genetic Variation Epigenetic Features
transcripts
dyna
mic
RNA-Sequencing Single Nucleotide Polymorphisms
Simple Sequence Repeats
DNA Methylation
Histone Modification
miRNA ExpressionExpression Microarrays
Amplified FragmentLength Polymorphisms
Gen
omic
D
ata
Type
sData Tables
stat
ic
Gene Annotations Sequence Motifs
Gene OntologiesPathwaysOrthologs
Transposable Elements
Interactions
Other species genomes
CpG statistics
Structural Elements
SizeGrowthLocation
EnvironmentStage
TreatmentTissueTraitStrain
Transcription Factors Binding Sites
Publications
Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...
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Phenotype
Epigenetics
Genetics Environment
Increased Growth Rate Tissue Quality
DiseaseResistance
Appearance
•Amplified Fragment Length Polymorphisms
•miRNA Expression
Temperature Diet
Fecundity
Yield
•Histone Modifications
•DNA Methylation Patterns
•Simple Sequence Repeats•Single Nucleotide Polymorphisms
G e n e Ex p r e s s i o
n
Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...
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Genome
Primary Data Table Groupings
Expressed Sequence Tags
Gene Expression Genetic Variation Epigenetic Features
transcripts
dyna
mic
RNA-Sequencing Single Nucleotide Polymorphisms
Simple Sequence Repeats
DNA Methylation
Histone Modification
miRNA ExpressionExpression Microarrays
Amplified FragmentLength Polymorphisms
Gen
omic
D
ata
Type
sData Tables
stat
ic
Gene Annotations Sequence Motifs
Gene OntologiesPathwaysOrthologs
Transposable Elements
Interactions
Other species genomes
CpG statistics
Structural Elements
SizeGrowthLocation
EnvironmentStage
TreatmentTissueTraitStrain
Transcription Factors Binding Sites
Publications
Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...
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Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...
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Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...
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Use Cases• Joining on Annotations• File Conversion• Querying Gene Tables
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Use Cases• Joining on Annotations• File Conversion• Querying Gene Tables
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Use Cases• Joining on Annotations• File Conversion• Querying Gene Tables
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Use Cases• Joining on Annotations• File Conversion• Querying Gene Tables
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Use Cases• Joining on Annotations• File Conversion• Querying Gene Tables
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Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...
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Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...github.com/sr320/qdod/wiki
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Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...github.com/sr320/qdod/wiki
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Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...github.com/sr320/qdod/wiki
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Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...github.com/sr320/qdod/wiki
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Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...
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Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
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Platforms
Open Science
Data
everything else...
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Biology
Environment
Molecular
Data Analysis
eScience
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Notebooks
Rationale
Platforms
Open Science
Data
everything else...
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Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...
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Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
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Platforms
Open Science
Data
everything else...
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Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...
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Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...
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Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...
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Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...
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Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...eagle.fish.washington.edu
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The Evolution of My Lab Notebook
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Open Notebook Science
... there is a URL to a laboratory notebook that is freely available and indexed on common search engines. It does not necessarily have to look like a paper notebook but it is essential that all of the information available to the researchers to make their conclusions is equally available to the rest of the world.
—Jean-Claude Bradley
Biology
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everything else...
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Open Notebook Science Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...
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Open Notebook Science
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Open Notebook Science
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Open Notebook Science
carlboettiger.info/lab-notebook
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Open Notebook Sciencegenefish.wikispaces.com
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Open Notebook Science
genefish.wikispaces.com
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Open Notebook Science
evernote.com/pub/che625/che625snotebook
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Open Notebook Science
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Open Notebook Science
Set some variables
blast
convert file format
upload to SQLShare (python client)
join in SQLShare - download
read in pandas
matplotlib generates graph of GOsllim
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Open Notebook Science Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...
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Open Notebook Science Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...
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Open Notebook Science Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...
a very new experiment
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Open Notebook Science Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...
a very new experiment
sr320.info
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Open Notebook Science Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...
a very new experiment
sr320.info
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Open Science
Biology
Environment
Molecular
Data Analysis
eScience
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Notebooks
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Platforms
Open Science
Data
everything else...
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Open Science
web-native scholarship
Biology
Environment
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eScience
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Notebooks
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Platforms
Open Science
Data
everything else...
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Photo credit: Flickr, Creative Commons, speechless
Sharing
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Example
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Example
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Example
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http://ivory.idyll.org/blog/
Biology
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http://ivory.idyll.org/blog/
Biology
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everything else...
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Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...
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Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...
![Page 73: Genomics on the Half Shell: Making Science more Open](https://reader036.fdocuments.us/reader036/viewer/2022062702/55496051b4c905e94e8b57a5/html5/thumbnails/73.jpg)
Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...robertslab.info
![Page 74: Genomics on the Half Shell: Making Science more Open](https://reader036.fdocuments.us/reader036/viewer/2022062702/55496051b4c905e94e8b57a5/html5/thumbnails/74.jpg)
Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...
Open Science Philosophy Transparency with limited effort
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Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...
Open Science Philosophy Transparency with limited effort will try just about anything
![Page 76: Genomics on the Half Shell: Making Science more Open](https://reader036.fdocuments.us/reader036/viewer/2022062702/55496051b4c905e94e8b57a5/html5/thumbnails/76.jpg)
Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...
![Page 77: Genomics on the Half Shell: Making Science more Open](https://reader036.fdocuments.us/reader036/viewer/2022062702/55496051b4c905e94e8b57a5/html5/thumbnails/77.jpg)
Biology
Environment
Molecular
Data Analysis
eScience
iPlant Galaxy
Notebooks
Rationale
Platforms
Open Science
Data
everything else...computationalproteomic.blogspot.com
Yasset Perez-Riverol en Wednesday, February 19, 2014
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Start them early
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Acknowledgements
Emma Timmins-Schiffman
Mackenzie GaveryClaire Olson
Sam WhiteBrent VadopalasJake Heare
Bill HoweDan Halperin
EPASTAR
Aquaculture Program
Saltonstall-Kennedyacidification
DNA methylation
oystergen.es/data
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