modencode: data and tools for the community - genome.gov · data.modencode.org...
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modENCODE data and tools
for the community
Gos Micklem University of Cambridge
www.modencode.org
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modENCODE DCC Data Flow modENCODE DCC data wranglers
submit data & meta-‐data
modENCODE DCC pipeline
QC vet
release
meta-‐data data
Faceted Browser modMine Amazon/Bionimbus
data.modencode.org intermine.modencode.org www.bionimbus.org 9p.modencode.org
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modENCODE Data Volume
2317 of 3763 datasets released: ~6 TB
Final freeze: expect ~20-‐25 TB altogether
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modENCODE Data Volume
2317 of 3763 datasets released: ~6 TB
Final freeze: expect ~20-‐25 TB altogether
Post-‐laptop era Nuisance to download
GEO/SRA (crude), WormBase/ FlyBase (refined) Amazon/ BioNimbus (all)
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www.modencode.org
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Faceted Browser: data.modencode.org
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9p.modencode.org
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GBrowse
Can save track combinations
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www.modmine.org
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www.modmine.org
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- Antibody names: PolII, H3K4me1, CP190 - Lab names: Reinke, Snyder- Combine terms with AND/AND NOT: fly AND embryo
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Growth
Chromatin preps
ChIP
Hybridisation
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Scanning
Normalisation
Enriched regions
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www.modmine.org
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lists in modMine
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fly gene expression from list
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StaFsFcal enrichment GO terms PublicaFons
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www.modmine.org
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www.modmine.org
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Science paperfigures
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“amazon modENCODE data” hHp://aws.amazon.com/datasets/8042906995278110
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NOTE: these snapshots only contained released data up to December 2011
AMI = Amazon Machine Image Mount everything, GBrowse, just data Pay as you go
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www.bionimbus.org
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Acknowledgments modENCODE DCC:
Nicole Washington, Seth Carbon, Ellen Kephart, Paul Lloyd, Chris Mungall, E.O. Stinson, Suzanna Lewis (LBNL)
Daniela Butano, Sergio Contrino, Fengyuan Hu, Rachel Lyne, Kim Rutherford, Richard Smith, Gos Micklem (Cambridge)
Angie Hinrichs, Jim Kent (UCSC)
Marc Perry, Peter Ruzanov, Quang Trinh, Zheng Zha, Lincoln Stein (OICR)
All the modENCODE data producers