Evolving Bits

Evolving BitsHilmar Lapp, NESCent

Feb 5, 2008

QuickTime™ and aAnimation decompressor

are needed to see this picture.

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