ICAR 2015 Workshop - Nick Provart

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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