Miller-PAGx - iPlant Pods

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4 Οκτ 2013 (πριν από 4 χρόνια και 9 μέρες)

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Enabling Phenotypic
I
mage Analysis

Using Shared
C
yberinfrastructure

Nathan Miller

Spalding Lab

UW
-
Madison

January 23, 2012

Small Scale Phenotypic Tool Kit



Few
phenotyping

platforms available

Large Scale Genetic Tool Kit


High throughput genomic sequencing


Reverse Genetic Populations Available


Bioinformatics


Structured Genetic Populations

for Statistical Genomic Work

Unbalanced Biological Tool Set

Introduction to the
phytoMorph


Project

Small Scale Phenotypic Tool Kit



Few
phenotyping

platforms available

Large Scale Genetic Tool Kit


High throughput genomic sequencing


Reverse Genetic Populations Available


Bioinformatics


Structured Genetic Populations

for Statistical Genomic Work

Unbalanced Biological Tool Set

Introduction to the
phytoMorph


Project


Common Biological Problem:

How Genotype maps to Phenotype


Small Scale Phenotypic Tool Kit



Few
phenotyping

platforms available

Large Scale Genetic Tool Kit


High throughput genomic sequencing


Reverse Genetic Populations Available


Bioinformatics


Structured Genetic Populations

for Statistical Genomic Work

Unbalanced Biological Tool Set

Introduction to the
phytoMorph


Project


Common Biological Problem:

How Genotype maps to Phenotype


Identify Bottleneck in Solving

This Problem

Small Scale Phenotypic Tool Kit



Few
phenotyping

platforms available

Large Scale Genetic Tool Kit


High throughput genomic sequencing


Reverse Genetic Populations Available


Bioinformatics


Structured Genetic Populations

for Statistical Genomic Work

Unbalanced Biological Tool Set

Help Balance via Machine Vision Technologies

Machine Vision:

Extracting meaningful Information from images

Infrared backlight

Close
-
focus
zoom lens
with visible
block/IR
-
pass
filter

CCD camera
firewire
-

connected to
an automated
workflow

Petri plate holder

In different rooms for different purposes we have approximately
30
of these
CCD cameras equipped to image Arabidopsis or maize seedling development
.

Help Balance via Machine Vision Technologies


70K price for~30
camera sets



~200 movies of
plants undergoing a
dynamic growth
process



Only 4GB a day





Camera and Data

In different rooms for different purposes we have approximately 20 of these
CCD cameras equipped to image Arabidopsis or maize seedling development
.

Help Balance via Machine Vision Technologies






High
-
Throughput
Phenotyping

of plant growth processes as they
unfold.


Changes the notion of a static phenotype to a watching a dynamic
process unfold.



As an example, brief focus on root
gravitropism
.





What can we do with a set of
camera banks?

What is
Gravitropism


Why is
Gravitropism

Important?

“Simple” Process of Bending Involves

Intra and Intercellular communication

Hormone Biology

Cell Division and Expansion

Water Relations

Signal Transduction and Transmission

Cell Specialization

Control Systems

Parent A

Parent B

Time course QTL: [
Landsberg

Erecta
] x [Cape Verde]

UW
-
Madison

Statistical Genetics

Applications

Reverse Genetic Screens

Doane

College

Genetics

of Plasticity

Penn State

Plant Cellular and Molecular
Biology

University

of Texas

Plant Cellular and Molecular
Biology

University of Florida

Maize Biology


Cold Spring Harbor

Class

Image

Analysis and
Phenotyping

Phytomorph
:
Enabling Phenotypic Image Analysis

Increase algorithms to include:

Seed Size:

Measure Arabidopsis Seed Size with flatbed scanner .


Tip Tracing:
Track a root and shoot apices for Rice, Arabidopsis, and Maize


Kinematics:

Measure spatiotemporal strain fields during growth.


Others……..

UW
-
Madison

Statistical Genetics

Applications

Reverse Genetic Screens

Doane

College

Statistical Genetics

of Plasticity

Penn State

Cellular and Molecular
Biology

University

of Texas

Reverse Genetics

University of Florida

Phenotypic Dependencies

Come full Circle:
Same problem but different type

Phytomorph
:
Enabling Phenotypic Image Analysis

UW
-
Madison

Statistical Genetics

Applications

Reverse Genetic Screens

Doane

College

Statistical Genetics

of Plasticity

Penn State

Cellular and Molecular
Biology

University

of Texas

Reverse Genetics

University of Florida

Phenotypic Dependencies

Phytomorph
:
Enabling Phenotypic Image Analysis

Come full Circle:
Same problem but different type

UW
-
Madison

Statistical Genetics

Applications

Reverse Genetic Screens

Doane

College

Statistical Genetics

of Plasticity

Penn State

Cellular and Molecular
Biology

University

of Texas

Reverse Genetics

University of Florida

Phenotypic Dependencies

Phytomorph
:
Enabling Phenotypic Image Analysis

%$@#
&!

Come full Circle:
Same problem but different type

UW
-
Madison

Statistical Genetics

Applications

Reverse Genetic Screens

Doane

College

Statistical Genetics

of Plasticity

Penn State

Cellular and Molecular
Biology

University

of Texas

Reverse Genetics

University of Florida

Phenotypic Dependencies

Phytomorph
:
Enabling Phenotypic Image Analysis
Using Shared
Cyberinfrastructure

%$@#
&!

Come full Circle:
Same problem but different type

Shared
Cyberinfrastructure

Two of many tools which are being hosted/provided by
iPlant

1)
AtmoSphere
: Cloud Computing

2)
iRODS
: Cloud Data Storage

AtmoSphere


Flexible tool for
customizing
machines for
software deployment

iRODS

@
iPlant


Common data
repository for Image
data

Shared
Cyberinfrastructure

University X


Securely Transfer data via
iDROP

to data store
(
iRODS@iPlant
)


Data can be
continously

syncronized

via
iDROP


Data can be pushed on
-
demand

iPlant


Handles user
authentication


Large Data storage


Receives data in Shared
environment


Allows
iPlant

users to
transfer data between labs

iRODS


Server

@
iPlant

#1

Shared
Cyberinfrastructure

University X


Login to
AtmoSphere

and
Start
phytoMorph

Machine

iPlant


Boot
-
Up Virtual
centOS

Linux


Handle Authentication

#2

Shared
Cyberinfrastructure

University X


Login to virtual Machine
and analyze data

iPlant


Allow for custom
software to be installed

#3

First Set of
phytoMorph

Algorithms

Brief List of Some Current Users

Won
Gyu

in Simon Gilroy’s Lab


500 GB of high resolution growth movies taken with

Desiree den Os in Gabriele
Monshausen’s

Lab


High Resolution movies of root growth


Seed size analysis


Used
phytoMorph@iPlant

Graduate Level Class:
Modern Techniques
and Concepts in Plant Cell Biology here at Penn State

Greg Clark and a team of students in Stan Roux’s Lab


High Resolution movies of root growth


Seed size analysis


Morphometric

Analysis

The described way of working is not what we hope for
but what is happening with a small set of beta groups.





Take a minute to thank them for being VERY patient
before
iPlant’s

infrastructure existed and while I learn
how to use
iPlant

CI.

Brief List of Some Current Users

Won
Gyu

in Simon Gilroy’s Lab


500 GB of high resolution growth movies.

Desiree den Os in Gabriele
Monshausen’s

Lab


High Resolution movies of root growth


Seed size analysis


Used
phytoMorph@iPlant

Graduate Level Class:
Modern Techniques
and Concepts in Plant Cell Biology at Penn State

Greg Clark and a team of students in Stan Roux’s Lab


High Resolution movies of root growth


Seed size analysis


Morphometric

Analysis

phytoBisque
:
Integration of Algorithms with Bisque

1)
Continue to deploy image processing methods.
iPlant

CI is an essential tool

to leverage.


2)
Free up users to work independent. If a single lab can be successful via machine

vision technologies, imagine what a community of Biologists can achieve.


3)
Free up me to continue my work in modeling complex traits.

Conclusions:

Staff:

Greg Abram

Sonali

Aditya

Roger
Barthelson

Brad Boyle

Todd Bryan

Gordon Burleigh

John
Cazes

Mike Conway

Karen Cranston

Rion

Doodey

Andy Edmonds

Dmitry
Fedorov

Michael
Gatto

Utkarsh

Gaur

Cornel
Ghiban

Michael Gonzales

Hariolf

Häfele

Matthew Hanlon

iPlant’s Building Blocks

74

Metadata

Data

Tools

Workflows

Viz

Executive Team:

Steve Goff

Dan
Stanzione

Faculty Advisors & Collaborators:

Ali
Akoglu

Greg Andrews

Kobus

Barnard

Sue Brown

Thomas
Brutnell

Michael
Donoghue

Casey Dunn

Brian
Enquist

Damian
Gessler

Ruth
Grene

John Hartman

Matthew Hudson

Dan
Kliebenstein

Jim
Leebens
-
Mack

David
Lowenthal

Robert
Martienssen

Students:

Peter Bailey

Jeremy Beaulieu

Devi Bhattacharya

Storme

Briscoe

Ya
-
Di Chen

John
Donoghue

Steven Gregory

Yekatarina

Khartianova

Monica Lent

Amgad

Madkour



B.S.
Manjunath


Nirav

Merchant

David Neale

Brian O’Meara

Sudha

Ram

David Salt

Mark
Schildhauer

Doug
Soltis

Pam
Soltis

Edgar Spalding

Alexis
Stamatakis

Ann Stapleton

Lincoln Stein

Val
Tannen

Todd Vision

Doreen Ware

Steve Welch

Mark
Westneat

Andrew
Lenards

Zhenyuan

Lu

Eric Lyons

Naim

Matasci

Sheldon McKay

Robert
McLay

Angel Mercer

Dave
Micklos

Nathan Miller

Steve Mock

Martha
Narro

Praveen
Nuthulapati

Shannon Oliver

Shiran

Pasternak

William
Peil

Titus
Purdin

J.A.
Raygoza

Garay

Dennis Roberts

Jerry Schneider

Anthony Heath

Barbara Heath

Matthew
Helmke


Natalie
Henriques

Uwe

Hilgert

Nicole Hopkins

Eun
-
Sook

Jeong

Logan Johnson

Chris Jordan

B.D. Kim

Kathleen Kennedy

Mohammed
Khalfan

Seung
-
jin

Kim

Lars
Koersterk

Sangeeta

Kuchimanchi

Kristian

Kvilekval

Aruna

Lakshmanan

Sue
Lauter

Tina Lee

Bruce
Schumaker

Sriramu

Singaram

Edwin Skidmore

Brandon Smith

Mary Margaret Sprinkle

Sriram

Srinivasan

Josh Stein

Lisa Stillwell

Kris
Urie

Peter Van Buren

Hans Vasquez
-
Gross

Matthew Vaughn

Fusheng

Wei

Jason Williams

John
Wregglesworth

Weijia

Xu

Jill
Yarmchuk

Aniruddha

Marathe

Kurt Michaels

Dhanesh

Prasad

Andrew
Predoehl

Jose
Salcedo

Shalini

Sasidharan

Gregory
Striemer

Jason
Vandeventer

Kuan

Yang


Postdocs
:

Barbara
Banbury

Jamie Estill

Bindu

Joseph

Christos
Noutsos


Brad
Ruhfel

Stephen A. Smith

Chunlao

Tang

Lin Wang

Liya

Wang

Norman
Wickett

Settles Lab

Muday

Lab

Spalding Lab

Ferrier


Lab

Durham Brooks Lab

Funding

Bisque Project