icar 2015 workshop - nick provart
TRANSCRIPT
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Araport: Bio-Analytic Resource Case Study
Nicholas Provart, Department of Cell and Systems
Biology & Centre for the Analysis of Genome
Evolution and Function, University of Toronto,
Canada
The Bio-Analytic Resource for Plant Biology
• BAR.utoronto.ca allows easy exploration of large biological data sets for hypothesis generation:
• 128,000 Single Nucleotide Polymorphisms
• 150 million gene expression measurements (75 million from A.th.)
• Documented subcellular localizations for 9.3k proteins, predicted localization for most of Arabidopsis proteome, from SUBA
• 70,944 predicted protein-protein interactions plus 36,306 documented PPIs
• 67,275 predicted protein tertiary structures and 700+ experimentally-determined structures
• Suite of easy-to-use tools for exploring these data
• Papers describing BAR tools have been cited ~2298 times
• Linked to and from by NCBI, TAIR, FLAGdb++, SIGnAL etc.
BAR
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Araport – Modules
International Arabidopsis Informatics Consortium (2012). The Plant Cell. 24(6): 2248-2256.
Zoomable
User Interface
Protein
Tertiary
Structure
Expressolog /
Synteny
Viewer
Arabidopsis eFP Browser
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BAR
eFP image
webservice
eFP Browser: Webservices
AraportThe Arabidopsis Information Portal
eFP Views in Araport
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Arabidopsis Interactions Viewer 2.0: Preparing for Araport
BAR
PSICQUIC
webservices
…
Arabidopsis Interactions Viewer 2.0
125 PPIs 171 PPIs
Matthew Ierullo, Provart Lab
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Araport Science Apps
Gene Slider: Exploring 90k Conserved Non-Coding Sequences
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Plant Regulome
Cell Reports 8: 2015-2030 (September 25, 2014)
Plant Regulome
Sullivan et al., 2014
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Gene Slider
Gene Slider
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Concept drawing for browsing RNA-Seq data
Collaboration with Ann Loraine, UNCC; Matt Vaughn, iPlant; Araport
BAM/BAI
archive at
iPlant
RNA-
Seq/eFP
engine
Extended IGB
Quickstart files
(metadata)
JBrowse/IGB etc.
Architecture for RNA-seq/eFP Browser
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ZUI Concept Drawing
Image courtesy of Jamie Waese, Provart Lab.
Spiral model redrawn from Cay Horstman: http://www.iro.umontreal.ca/~pift1025/bigjava/Ch17/ch17.html
Agile Development Process
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Spiral model redrawn from Cay Horstman: http://www.iro.umontreal.ca/~pift1025/bigjava/Ch17/ch17.html
Fucile..Provart (2011)
Agile Development Process
Spiral model redrawn from Cay Horstman: http://www.iro.umontreal.ca/~pift1025/bigjava/Ch17/ch17.html
Fucile..Provart (2011)
Waese..Provart (2014)
Agile Development Process
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Spiral model redrawn from Cay Horstman: http://www.iro.umontreal.ca/~pift1025/bigjava/Ch17/ch17.html
Fucile..Provart (2011)
Waese..Provart (2014)
Waese..Provart (2015)
Agile Development Process
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User Testing – help us improve ePlant!
Bio-Analytic Resource Booth 11A
Jamie Waese
http:/bar.utoronto.ca/eplant
BAR
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50 Years of Arabidopsis Research Explorer App
Kiana Toufighi
Ryan Austin
Siobhan Brady
Asher Pasha
Nina Wang
Hardeep Nahal
Joe Wu
Rohan Patel
Matthew Ierullo
Ron Ammar
Ben Vinegar
Debbie Winter
Richard Song
Anjali Silva
David Di Biase
Geoff Fucile
Jamie Waese
Hans Yu
Jim Fan
Fausto de Oliveira
Sylva Donaldson
Acknowledgements
BAR
Ron Ammar
http://www. bar .utoronto.caBAR
• BAR.utoronto.ca allows easy exploration of large biological data sets for hypothesis generation:
• 128,000 Single Nucleotide Polymorphisms
• 150 million gene expression measurements (75 million from A.th.)
• Documented subcellular localizations for 9.3k proteins, predicted localization for most of Arabidopsis proteome, from SUBA
• 70,944 predicted protein-protein interactions plus 36,306 documented PPIs (rice interologs also available!)
• 67,275 predicted protein tertiary structures and 700+ experimentally-determined structures