Genomics on the Half Shell: Making Science more Open

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Genomics on theHalf Shell: Making Science more Open Steven B. Roberts Associate Professor School of Aquatic and Fishery Sciences University of Washington robertslab.info

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Open Science •You arefree to Share! •Our lab practices open notebook science •Slides and more available @ oystergen.es/data

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Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms OpenScience Data everything else...

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e Transcriptome Proteome DNA Methylation

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e Biology Environment Ocean Acidification Elevated pCO2causes developmental delay in early larval Paciﬁc oysters, Crassostrea gigas. Timmins-Schiffman et al 2012

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e Shotgun Proteomics Biology Environment Ocean Acidification 10.1093/conphys/cot009

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e Biology Shotgun Proteomics Environment Molecular Data Analysis eScience iPlantGalaxy Notebooks Rationale Platforms Open Science Ocean Acidification Data everything else... eagle.ﬁsh.washington.edu/emma

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e Biology Environment Molecular Data Analysis Transcriptome Proteome DNA Methylation eScience iPlant Galaxy Notebooks Rationale Platforms OpenScience Data everything else...

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Biology Environment Molecular Data Analysis eScience Function? iPlant Galaxy Notebooks Rationale Platforms OpenScience Data everything else...

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Photo credit: Flickr,Creative Commons, dkeats mosaic associated with gene bodies

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Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale HiSeq- lane - 70G mapping - 60G table Platforms Open Science Data everything else...

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Stochastic Variation Biology Environment Molecular Data Analysis eScience iPlantGalaxy Notebooks Rationale Platforms Open Science Data 10.1093/bfgp/elt054 10.6084/m9.ﬁgshare.880763 everything else...

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Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale raw- 70G mapping - 60G tables - 40G ........ Platforms Open Science Data everything else...

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Biology Environment Publications Interactions static Pathways Data Tables Gene Annotations Size Growth Location Environment Stage Treatment Tissue Trait Strain Molecular CpGstatistics Transposable Elements Sequence Motifs Transcription Factors Binding Sites transcripts Gene Expression Genomic Data Types Primary Data Table Groupings Structural Elements Other species genomes Genome dynamic Orthologs Gene Ontologies Data Analysis eScience iPlant Galaxy Genetic Variation Epigenetic Features Notebooks Rationale RNA-Sequencing Single Nucleotide Polymorphisms DNA Methylation Expressed Sequence Tags Ampliﬁed Fragment Length Polymorphisms Expression Microarrays Simple Sequence Repeats Platforms Histone Modiﬁcation Open Science miRNA Expression Data everything else...

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Biology Environment Yield Phenotype Increased Growth Rate G e ne E Genetics xp re Fecundity si s Appearance Molecular Disease Resistance Data Analysis TissueQuality eScience on iPlant Galaxy Notebooks Epigenetics •DNA Methylation Patterns •miRNA Expression •Histone Modiﬁcations •Single Nucleotide Polymorphisms •Simple Sequence Repeats •Ampliﬁed Fragment Length Polymorphisms Environment Temperature Rationale Platforms Diet Open Science Data everything else...

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Biology Environment Publications Interactions static Pathways Data Tables Gene Annotations Size Growth Location Environment Stage Treatment Tissue Trait Strain Molecular CpGstatistics Transposable Elements Sequence Motifs Transcription Factors Binding Sites transcripts Gene Expression Genomic Data Types Primary Data Table Groupings Structural Elements Other species genomes Genome dynamic Orthologs Gene Ontologies Data Analysis eScience iPlant Galaxy Genetic Variation Epigenetic Features Notebooks Rationale RNA-Sequencing Single Nucleotide Polymorphisms DNA Methylation Expressed Sequence Tags Ampliﬁed Fragment Length Polymorphisms Expression Microarrays Simple Sequence Repeats Platforms Histone Modiﬁcation Open Science miRNA Expression Data everything else...

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Use Cases • Joiningon Annotations • File Conversion • Querying Gene Tables

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Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms OpenScience Data github.com/sr320/qdod/wiki everything else...

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Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms OpenScience Data everything else... eagle.ﬁsh.washington.edu

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The Evolution ofMy Lab Notebook

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Open Notebook Science Biology Environment ...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. Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data —Jean-Claude Bradley everything else...

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Open Notebook Science Biology Environment Molecular DataAnalysis 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 carlboettiger.info/lab-notebook

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Open Notebook Science geneﬁsh.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 Setsome 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 avery new experiment Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...

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Open Notebook Science avery new experiment Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data sr320.info everything else...

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Open Notebook Science avery new experiment Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data sr320.info everything else...

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Biology Environment Molecular Data Analysis Open Science eScience iPlantGalaxy Notebooks Rationale Platforms Open Science Data everything else...

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Biology Environment Molecular Data Analysis Open Science eScience iPlantGalaxy Notebooks Rationale Platforms web-native scholarship Open Science Data everything else...

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Sharing Photo credit: Flickr,Creative Commons, speechless

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Example

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Example

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Example

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Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms OpenScience Data http://ivory.idyll.org/blog/ everything else...

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Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms OpenScience Data http://ivory.idyll.org/blog/ everything else...

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Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms OpenScience Data robertslab.info everything else...

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Open Science Philosophy Transparencywith limited effort Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...

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Open Science Philosophy Transparencywith limited effort will try just about anything Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...

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Biology Environment Molecular Yasset Perez-Riverol enWednesday, February 19, 2014 Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else... computationalproteomic.blogspot.com

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Start them early

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Acknowledgements Emma Timmins-Schiffman Mackenzie Gavery ClaireOlson Sam White Brent Vadopalas Jake Heare Bill Howe Dan Halperin DNA methylation acidiﬁcation Saltonstall-Kennedy EPA STAR Aquaculture Program oystergen.es/data

Genomics on the Half Shell: Making Science more Open

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Genomics on the Half Shell: Making Science more Open