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BactoGeNIE talk at Friendly Friday

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visualizing lots of genomes on big displays

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BactoGeNIE talk at Friendly Friday

  1. 1. Toward a 1000-genome visualization for scalable resolution display environments Jillian Aurisano April 12, 2013
  2. 2. The birth of genomics • A decade ago: – First complete human genome sequence released. – 13 years and 2.7 billion dollars to generate the sequence the 3.3 billion nucleotides in the human genome. – Intensive work for years to identify the 26,000 genes in this sequence
  3. 3. Genome sequencing boom • Since 2003: – Sequencing costs have decreased faster than Moore’s Law • Today: – 1000-genome project – Thousands of bacterial strains sequenced – Metagenomics
  4. 4. As a result • Scalable computational approaches to genome analysis needed – Lots of progress in data mining, bioinformatics, parallel algorithms, cloud computing But – More work needed to develop scalable genome visualization approaches • Why is visualization important? – 1/3 of human brain devoted to processing visual information – Keep expert ‘in the loop’ to verify computational results – Human experts needed to translate data  knowledge
  5. 5. Technical opportunity • High resolution displays – High density information presentation is possible • Large, high-resolution displays – Multiple high-density visualizations can be juxtaposed and compared • Multi-user environments – Collaborative data analysis and data set mashups • New visualization paradigm, opportunity for new visualization approaches
  6. 6. Specific sub-problem: analyzing local variations in gene content • Help bacterial genomics researchers look for conserved sets of genes in bacterial genomes • Why: In bacterial genomes, genes that occur close to each other in the genome may be functionally connected. • Also: Differences in gene content and order in related bacterial strains have evolutionary implications
  7. 7. Other approaches: browsers Pubmed: UCSD genome browser
  8. 8. Other approaches: large scale comparisons in circular representation Circos: An information aesthetic for comparative genomics
  9. 9. GeneRiViT
  10. 10. Goals • New type of genome visualization approach that is: – Scalable: not just comparing 4 genomes, but hundreds • Less text; high density presentation; – Interactive: enable analysis of these bacterial strains – Flexible: not locked to one reference coordinate system; genomes reorderable – Connected: Links between similar elements are shown to enable comparisons
  11. 11. How my prototype works • User specifies 2 types of files: – Genome features: start, stop coordinates of genes and other genome elements. Additional annotation info. – Sequence file: sequences of these genome features • A genome for one species not always in one piece • Use algorithm (cd-hit) to cluster sequences based on similarity • Create a local database, cache a subset to visualize
  12. 12. Demo
  13. 13. What’s next • Lots of analysis features I’d like to explore • Then port this to run on the wall in EVL cybercommons • Long term: Build it into an integrative genomics vis framework for large, high-resolution environments
  14. 14. GenoSAGE • Multiple high-resolution genome visualization in one view, plus associated visualizations of other data types – Can view data at multiple levels of detail – Evaluate details in context • Connections between visualizations – Integration across visualizations • Spatial organization of visualizations to encode information • Multi-user visualization environment
  15. 15. Thanks! • Questions? • Contact me at: jauris2@uic.edu (my other project)

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