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Bottoms bosc2010 bio_snp_inherit

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Bottoms bosc2010 bio_snp_inherit

  1. 1. SNP Allele Designations (Bio::SNP::Inherit) Christopher Bottoms BOSC 2010
  2. 2. 5 million data “items” one CPU: 2+ days eight CPUs: 1-2 days
  3. 3. SNP ID Sample ID Base1 Base2 1 1 A A 1 2 A A 1 3 A G … … … … 1 5000 A A 2 1 C C … … … … … … … … 1106 5000 GG GG
  4. 4. SNP ID Sample ID Base1 Base2 1 1 A A 1 2 A A 1 3 A G … … … … 1 5000 A A 2 1 C C … … … … … … … … 1106 5000 GG GG
  5. 5. “ Matrix” data file format SNP ID 1 2 3 … 5000 SNP1 AA AA AG … AA SNP2 CC GG GG … CG
  6. 6. “ Matrix” data file format SNP ID 1 2 3 … 5000 SNP1 AA AA AG … AA SNP2 CC GG GG … CG
  7. 7. Using new data format <ul><li>12 million data items </li></ul><ul><li>one cpu: ~30 min </li></ul>
  8. 8. ID’s file ID Name Group 1 B73 B73 2 B73xZ1 NAMF1 3 Mo17 Control 4 M100 IBM 5 Bob B73xZ1
  9. 9. ID’s file ID Name Group 1 B73 B73 2 B73xZ1 NAMF1 3 Mo17 Control 4 M100 IBM 5 Bob B73xZ1
  10. 10. “ Human Parsed” ID’s file ID Name Group A (ID) B (ID) AxB (ID) 1 B73 B73 2 B73xZ1 NAMF1 3 Mo17 Control 4 M100 IBM 1 3 5 Bob B73xZ1 1 2
  11. 11. Lessons learned <ul><li>Explore other solutions before deciding on parallel processing </li></ul><ul><li>File format changes can simplify work </li></ul><ul><li>When appropriate, divide work </li></ul><ul><ul><li>Humans: Complicated but “once-only” task </li></ul></ul><ul><ul><li>Computers: Repetitive boring work </li></ul></ul>
  12. 12. Acknowledgements <ul><li>Advisors </li></ul><ul><li>Mike McMullen </li></ul><ul><li>Sherry Flint-Garcia </li></ul><ul><li>Hardware support </li></ul><ul><li>Arturo Garcia </li></ul><ul><li>Funding </li></ul><ul><ul><li>National Science Foundation Plant Genome Program Grant DBI-0820619 </li></ul></ul><ul><ul><li>USDA-ARS </li></ul></ul>
  13. 13. Acknowledgements <ul><li>Programming support </li></ul><ul><li>You (CPAN) </li></ul><ul><li>You (stackoverflow.com) </li></ul><ul><li>You (perlmonks.org) </li></ul>
  14. 14. End

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