Genomics on the Half Shell: Making Science more Open

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Abstract
Technology has significantly changed how research is done in biology. Along with this shift, it is increasingly easier and advantageous to operate in an open science framework. In this presentation I will begin by providing an overview of our research efforts with particularly attention to challenges in data analysis. Research in our lab focuses on characterizing physiological responses of shellfish to environmental change, examining impacts and adaptive potential from the nucleotide to organism level. A core component of this includes investigating the functional relationship of genetics, epigenetics, and transcription. In our research we leverage several computing infrastructure solutions that I will describe. In addition, our lab practices Open Notebook Science. I will describe the practical aspects of how we accomplish this including addressing some of the concerns and realized advantages. Beyond online lab notebooks, we are continually experimenting with different ways to use online resources to engage with a larger audience and improve science communication. I have found this is a complex balance of time and effort versus impact and will discuss how our lab group attempts to reach this balance.

Bio
Steven Roberts is an Associate Professor in the School of Aquatic and Fishery Sciences where his research centers around characterizing the response of aquatic organisms to environmental change. Prior to coming to the University of Washington, in 2007 he was at the Marine Biological Laboratory in Woods Hole, Massachusetts and received his PhD from the University of Notre Dame. In graduate school he spent most of his time transferring agarose gels, and now he spends most of his time transferring files.

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Genomics on the Half Shell: Making Science more Open

  1. 1. Genomics on the Half Shell: Making Science more Open Steven B. Roberts Associate Professor School of Aquatic and Fishery Sciences University of Washington robertslab.info
  2. 2. Open Science •You are free to Share! •Our lab practices open notebook science •Slides and more available @ oystergen.es/data
  3. 3. Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...
  4. 4. Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...
  5. 5. e
  6. 6. e Transcriptome Proteome DNA Methylation
  7. 7. e Biology Environment Ocean Acidification Elevated pCO2 causes developmental delay in early larval Pacific oysters, Crassostrea gigas. Timmins-Schiffman et al 2012
  8. 8. e Shotgun Proteomics Biology Environment Ocean Acidification 10.1093/conphys/cot009
  9. 9. e Biology Shotgun Proteomics Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Ocean Acidification Data everything else... eagle.fish.washington.edu/emma
  10. 10. e Biology Environment Molecular Data Analysis Transcriptome Proteome DNA Methylation eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...
  11. 11. Biology Environment Molecular Data Analysis eScience Function? iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...
  12. 12. Photo credit: Flickr, Creative Commons, dkeats mosaic associated with gene bodies
  13. 13. Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale HiSeq - lane - 70G mapping - 60G table Platforms Open Science Data everything else...
  14. 14. Stochastic Variation Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data 10.1093/bfgp/elt054 10.6084/m9.figshare.880763 everything else...
  15. 15. Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...
  16. 16. Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...
  17. 17. Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale raw - 70G mapping - 60G tables - 40G ........ Platforms Open Science Data everything else...
  18. 18. Biology Environment Publications Interactions static Pathways Data Tables Gene Annotations Size Growth Location Environment Stage Treatment Tissue Trait Strain Molecular CpG statistics 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...
  19. 19. Biology Environment Yield Phenotype Increased Growth Rate G e ne E Genetics xp re Fecundity si s Appearance Molecular Disease Resistance Data Analysis Tissue Quality 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...
  20. 20. Biology Environment Publications Interactions static Pathways Data Tables Gene Annotations Size Growth Location Environment Stage Treatment Tissue Trait Strain Molecular CpG statistics 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...
  21. 21. Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...
  22. 22. Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...
  23. 23. Use Cases • Joining on Annotations • File Conversion • Querying Gene Tables
  24. 24. Use Cases • Joining on Annotations • File Conversion • Querying Gene Tables
  25. 25. Use Cases • Joining on Annotations • File Conversion • Querying Gene Tables
  26. 26. Use Cases • Joining on Annotations • File Conversion • Querying Gene Tables
  27. 27. Use Cases • Joining on Annotations • File Conversion • Querying Gene Tables
  28. 28. Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...
  29. 29. Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data github.com/sr320/qdod/wiki everything else...
  30. 30. Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data github.com/sr320/qdod/wiki everything else...
  31. 31. Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data github.com/sr320/qdod/wiki everything else...
  32. 32. Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data github.com/sr320/qdod/wiki everything else...
  33. 33. Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...
  34. 34. Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...
  35. 35. Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...
  36. 36. Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...
  37. 37. Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...
  38. 38. Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...
  39. 39. Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...
  40. 40. Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...
  41. 41. Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...
  42. 42. Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else... eagle.fish.washington.edu
  43. 43. The Evolution of My Lab Notebook
  44. 44. 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...
  45. 45. Open Notebook Science Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...
  46. 46. Open Notebook Science
  47. 47. Open Notebook Science
  48. 48. Open Notebook Science carlboettiger.info/lab-notebook
  49. 49. Open Notebook Science genefish.wikispaces.com
  50. 50. Open Notebook Science genefish.wikispaces.com
  51. 51. Open Notebook Science evernote.com/pub/che625/che625snotebook
  52. 52. Open Notebook Science
  53. 53. 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
  54. 54. Open Notebook Science Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...
  55. 55. Open Notebook Science Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...
  56. 56. Open Notebook Science a very new experiment Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...
  57. 57. Open Notebook Science a very new experiment Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data sr320.info everything else...
  58. 58. Open Notebook Science a very new experiment Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data sr320.info everything else...
  59. 59. Biology Environment Molecular Data Analysis Open Science eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...
  60. 60. Biology Environment Molecular Data Analysis Open Science eScience iPlant Galaxy Notebooks Rationale Platforms web-native scholarship Open Science Data everything else...
  61. 61. Sharing Photo credit: Flickr, Creative Commons, speechless
  62. 62. Example
  63. 63. Example
  64. 64. Example
  65. 65. Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data http://ivory.idyll.org/blog/ everything else...
  66. 66. Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data http://ivory.idyll.org/blog/ everything else...
  67. 67. Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...
  68. 68. Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...
  69. 69. Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data robertslab.info everything else...
  70. 70. Open Science Philosophy Transparency with limited effort Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...
  71. 71. Open Science Philosophy Transparency with limited effort will try just about anything Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...
  72. 72. Biology Environment Molecular Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else...
  73. 73. Biology Environment Molecular Yasset Perez-Riverol en Wednesday, February 19, 2014 Data Analysis eScience iPlant Galaxy Notebooks Rationale Platforms Open Science Data everything else... computationalproteomic.blogspot.com
  74. 74. Start them early
  75. 75. Acknowledgements Emma Timmins-Schiffman Mackenzie Gavery Claire Olson Sam White Brent Vadopalas Jake Heare Bill Howe Dan Halperin DNA methylation acidification Saltonstall-Kennedy EPA STAR Aquaculture Program oystergen.es/data

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