evolving bits
DESCRIPTION
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. - PowerPoint PPT PresentationTRANSCRIPT
Evolving BitsHilmar Lapp, NESCent
Feb 5, 2008
QuickTime™ and aAnimation decompressor
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WATORA.K. Dewdney (1984) Sharks and fish wage an ecological war on the
toroidal planet Wa-Tor, Scientific AmericanApplet by Larry Leinweber
Real-Time Data Acquisition
The Advent of Genome-Wide Scale(Note: I wasn’t involved in Genome Sequencing)
Oligonucleotide Fingerprinting
Image Analysis
The Need for Data Integration
Lab Biology is Gene-Centric
Feature Graphs, orThe Platonic Gene Concept
6850(LocusLink)
GNF055813(GNF cDNA clones)
hCG29698 (Celera)
P43405 (UniProt)
NP_003168 (RefSeq)
NP_003168 (RefSeq)
NM_003177(RefSeq)
hCT1962558 (Celera)
hCT20865 (Celera)
207540_s_at (HG-U133A)
Hs.192182 (UniGene)
ENSG00000165025 (Ensembl)
ENST00000297685 (Ensembl)
36885_s_at (HG_U95Av2)
Reagents are part of the picture
Biology needs Functional Data
Data & Annotation Pipelines
““when the genome project was foundering in a sea when the genome project was foundering in a sea of incompatible data formats, rapidly-changing of incompatible data formats, rapidly-changing techniques, and monolithic data analysis programs techniques, and monolithic data analysis programs […], Perl saved the day.” […], Perl saved the day.”
Lincoln Stein, Human Genome Project, 1996
““when the genome project was foundering in a sea when the genome project was foundering in a sea of incompatible data formats, rapidly-changing of incompatible data formats, rapidly-changing techniques, and monolithic data analysis programs techniques, and monolithic data analysis programs […], Perl saved the day.” […], Perl saved the day.”
Lincoln Stein, Human Genome Project, 1996
ClustalW
CommonObject Model
Phylip
ProgramWrappers
IO FormatReaders +
Writers
execute
Write inputParse output
Reusable Code for the Life Sciences
Pooling Efforts to Achieve Excellence
Interoperability: Standards, APIs, Reusable Code
Open Development
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