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Evolving Bits

Evolving Bits. Hilmar Lapp, NESCent Feb 5, 2008. WATOR A.K. Dewdney (1984) Sharks and fish wage an ecological war on the toroidal planet Wa-Tor, Scientific American Applet by Larry Leinweber. Real-Time Data Acquisition.

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Evolving Bits

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  1. Evolving Bits • Hilmar Lapp, NESCent • Feb 5, 2008

  2. WATORA.K. Dewdney (1984) Sharks and fish wage an ecological war on the toroidal planet Wa-Tor, Scientific AmericanApplet by Larry Leinweber

  3. Real-Time Data Acquisition

  4. The Advent of Genome-Wide Scale(Note: I wasn’t involved in Genome Sequencing)

  5. Oligonucleotide Fingerprinting

  6. Image Analysis

  7. The Need for Data Integration

  8. Lab Biology is Gene-Centric

  9. hCG29698 (Celera) Hs.192182 (UniGene) 6850 (LocusLink) hCT1962558 (Celera) hCT20865 (Celera) P43405 (UniProt) NM_003177 (RefSeq) ENSG00000165025 (Ensembl) NP_003168 (RefSeq) ENST00000297685 (Ensembl) GNF055813 (GNF cDNA clones) 207540_s_at (HG-U133A) 36885_s_at (HG_U95Av2) Feature Graphs, orThe Platonic Gene Concept

  10. Reagents are part of the picture

  11. Biology needs Functional Data

  12. execute IO FormatReaders +Writers Phylip ClustalW ProgramWrappers Common Object Model Write input Parse output “when the genome project was foundering in a sea of incompatible data formats, rapidly-changing techniques, and monolithic data analysis programs […], Perl saved the day.” Lincoln Stein, Human Genome Project, 1996 Data & Annotation Pipelines

  13. Reusable Code for the Life Sciences

  14. Pooling Efforts to Achieve Excellence

  15. Interoperability: Standards, APIs, Reusable Code

  16. Open Development

  17. Acknowledgments: • Bio*: Jason Stajich, Ewan Birney, Lincoln Stein, Aaron Mackey, Chris Mungall, and many others • Novartians: András Aszódi, Serge Batalov, John Walker, John Hogenesch, and many others • NESCent: Todd Vision, Kathleen Smith, and too many evolutionary biologists to enumerate

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