VISG Session 2009Phillip Wilcox, Rod Ball, Gail Timmerman-Vaughan, Benoit Auvray ,Sammie Jia,

Mik Black

Why is the Virtual Institute of Statistical Genetics Important?•A MapNet initiative…

•MapNet participants are the key end-users

•Your tax $ are paying for it!

VISG Session…•3:20pm - Update: Virtual Institute of Statistical Genetics.

Phillip Wilcox (Scion)

•3.35pm - VISG polyploids. Phillip Wilcox (Scion), Gail Timmerman-Vaughan and YiLin (Sammie) Jia (Plant and Food Research)

•3.55pm - VISG Large datasets project.Benoit Auvray & Ken Dodds (AgResearch)

•4.15pm - eResearch Resources for VISG.Mik Black (University of Otago)

•4.35pm - Wrap-up and feedback.Phillip Wilcox (Scion)

Contents

1. Background & rationale - PW

2. Structure - PW

3. FRST Contract: Milestones - PW

4. Progress reports…PW, RB, GTV,

5. Wrap up…

1. Background… what is the VISG?

•‘Virtual Institute of Statistical Genetics’

•FRST funded @ $NZ 938 K per annum NERF NZS portfolio Viewed as important cross-sector

underpinning capability

1. Background cont’d

•5 year FRST-funded Oct 1 2008•Participants: Scion, ESR Ltd, Universities of Auckland and Otago, AgResearch, Plant and Food Research, ViaLactia Biosciences Ltd •End users = NZ gene mapping scientists in various sector-specific programmes

Why?

• New genomics technologies = LARGE datasets generated VERY quickly - New analytical and data handling challenges

• Need valid statistical inference…- Computationally intensive Bayesian methods

• Underpinning NZ science capability with multi-sector applicability

- Diagnostic tools from gene mapping already in market place

How?

eResearch: Statisticians + end-user geneticists working together from multiple organisations across NZ in project teams…

- KAREN- Grid Computing - Shared data storage- Communication tools for virtual teams…

1. Background cont’d - FRST Contract…

The aim is to ‘establish NZ as a world leader in advanced statistical methods for gene mapping’ by 2014. This will be achieved by:

‘establishing a Virtual Institute of Statistical Genetics’ combining NZs top gene mapping statisticians with geneticists to develop advanced methods for experimental design and analysis using pan-NZ computational platforms (KAREN and BeSTGRID)’.

1. Background cont’d - FRST Contract…The key steps involve:

Developing analytical methods in large scale data analysis and experimental design, relevant for future gene mapping applications.

Testing the methods using NZ-specific datasets from sector oriented RFI and HRC-funded programmes.

Developing software for use in RFI, HRC and industry breeding programmes

The outcome will be based on: Development of new methods, globally recognised

through peer review and application in sector-specific programmes in NZ, building NZ's reputation in biological sciences and international competitiveness in biologically-based sectors.

1. Background cont’d – FRST Contract – Nine Milestones

1.1 Establish project governance group by Feb 28 091.2 Establish project teams by March 30 20091.3 Establish HPC and data storage needs by June 30 20091.4 Establish eResearch portal by August 30 20101.5 Project 1 – Predicting phenotype from ‘Large Data Sets’ –

complete June 30 20121.6 Project 2 – ‘Polyploid’ QTL mapping – complete by end of 20111.7 Project 3 – Innovative Experimental designs – January 2009 –

Sep 30 20131.8 Project 4a – Project analysis Oct 2010 – Janu 20111.9 Project 4b – Method development and implementation Feb

2011- Sept 30 2013

Statisticians

Geneticists

2. VISG Structure

Governance

Management

Administration

IP Management

Group*

Project Governance

Group

Programme Leader (PW)

Scion

•Financial Services

•Legal Services

•FRST interactions

•Project support

•HR

Science

Rod Ball

Ken Dodds

Bernoit Auvray

Mik Black

David Chagne

John McCallum

Phillip Wilcox

Paul Fisher

Rod Ball

Yi Lin Jia

Nihal DeSilva

Gail Timmerman-Vaugh

Mark McNeilage

Brent Barret

Rod BallKen DoddsBernoit AuvaryMik Black

Phillip Wilcox Rod LeaDavid ChagnePhD student

Sharon Browning

Rod Ball

Gail Timmerman –Vaughan

Paul Fisher

Geoff Gill

David Chagne

PhD student

Projects Large Datasets Polyploids Experimental “Project 4” eResearch QTL Mapping Design Portal

Mik Black

Phillip Wilcox

3. Milestone Progress…

1.1 PGG group established: membership agreed. Terms of Reference agreed. Two meetings held (November ‘08, May ‘09).

1.2 Project teams team composition decided & roles agreed some changes in teams

1.3 HPC and data storage needs: Won’t know exact needs until projects underway BUT have secured access to BeSTGRID and UoC supercomputing

infrastructure

Project GovernanceRoles Assure science is

appropriately positioned Ensure science is of

international quality Provide recommendations

for commercialisation (or not) of intellectual property

Review research progress and steer research directions

Members Prof Bruce Weir (UoWashington) Prof Peter Visscher (QIMR) Elspeth MacRae (Scion) Phillip Wilcox (Scion) Tony Merriman (UoOtago) Gail Timmerman-Vaughan (Plant and Food)

IP Management

•Contributed IP recorded in IP register

• IP management group proposed determine IF & how new IP should be commercialised 1 representative per collaborating organisation

3. Milestone Progress…

1.1 PGG group established: membership agreed. Terms of Reference agreed. Two meetings held (November ‘08, May ‘09).

1.2 Project teams team composition decided & roles agreed some changes in teams

1.3 HPC and data storage needs: Won’t know exact needs until projects underway BUT have secured access to BeSTGRID and UoC supercomputing

infrastructure

3. Milestone Progress…

1.1 PGG group established: membership agreed. Terms of Reference agreed. Two meetings held (November ‘08, May ‘09).

1.2 Project teams team composition decided & roles agreed some changes in teams

1.3 HPC and data storage needs: Won’t know exact needs until projects underway BUT have secured access to BeSTGRID and UoC supercomputing

infrastructure

3. Milestone Progress…1.4 Deployment and Implementation of eResearch portal

underway. Mik Black leading this & will update Developing a Sakai-based portal, first version in use.

1.5 Large Data Sets project – Rod/Benoit/Ken to update.

1.6 Polyploids QTL mapping project – Rod/PW/Sammie/Gail to update

1.7-1.9 Milestones are not current.

Also:• Recruiting PhD students (2)

3. Milestone Progress…1.4 Deployment and Implementation of eResearch portal

underway. Mik Black leading this & will update Developing a Sakai-based portal, first version in use.

1.5 Large Data Sets project – Rod/Benoit/Ken to update.

1.6 Polyploids QTL mapping project – Rod/PW/Sammie/Gail to update

1.7-1.9 Milestones are not current.

Also:• Recruiting PhD students (2)

4. Progress Reports: Some things for you to think about…

1. How should VISG interact with the wider MapNet?

2. How should VISG communicate it’s progress to the wider MapNet?

3. How should VISG obtain feedback from MapNet?

4. Format for future presentations?• As part of the annual MapNet workshop?• KAREN/Video conferencing on an as-needed basis?

VISG Session…• 3:20pm - Update: Virtual Institute of Statistical Genetics.

Phillip Wilcox (Scion)

• 3.35pm - VISG polyploids. Phillip Wilcox (Scion), Gail Timmerman-Vaughan and YiLin (Sammie)

Jia (Plant and Food Research)

• 3.55pm - VISG Large datasets project.Benoit Auvray & Ken Dodds (AgResearch)

• 4.15pm - eResearch Resources for VISG.Mik Black (University of Otago)

• 4.35pm - Wrap-up and feedback.Phillip Wilcox (Scion)

Overall VISG Progress in first 10 months…

• All projects started and on track All 08-09FY milestones met

• First version of eResearch portal now online

• Project Governance Group established and operating (2 meetings so far)

• Terms of collaboration agreed to…

• Annual report submitted to FRST

Tasks 09-10• Formalise collaboration agreement• Formalise subcontracts• Progress science in LDS and polyploids projects• Set up new project – ‘Experimental Design’• Recruit PhD student• Complete eResearch portal• Establish IP register• Parallelisation course + grid computing (Oct or Nov)• plus many more…

Some things for you to think about…

1. How should VISG interact with the wider MapNet?

2. How should VISG communicate it’s progress to the wider MapNet?

3. How should VISG obtain feedback from MapNet?

4. Format for future presentations?• As part of the annual MapNet workshop?• KAREN/Video conferencing on an as-needed basis?

MapNet Activities 2008-2009

• VISG has dominated, relatively few other activities

• David Chagne’s Marsden proposal on CNV Involved a number of MapNet participants

• Victoria University has joined ‘officially’ represented by Dr Nokuthaba Sibanda (Bayesian

statistician)

MapNet 2009 onwards

•Steering committee Membership needs reviewing Some replacements required New participating

organisations

•A new convenor is required…

Steering Committee – Current Membership• Scion - Dr Philip Wilcox (Convener); • AgResearch - Dr Paul Fisher (Invermay), Brent Barrett (Grasslanz); • HortResearch - David Chagne (Palmerston North), Nnadozie

Oraguzie (Hastings); • University of Canterbury - Dr Neil Gemmell; • University of Otago - Dr Tony Merriman; • University of Auckland - Dr Sharon Browning; • Crop and Food Research - Dr Gail Timmerman-Vaughan

(Christchurch); • ESR - Dr Rod Lea; • ViaLactia Biosciences ltd - Geoff Gill; • Livestock Improvement Corporation - Dr Juan Arias; • Victoria University – Dr Nokuthaba Sibanda

Next Workshop – where and when?

•Back to the North Island?

•Combine with Australians for a meeting?

WEST ISLAND

The End

Now drink up!(it’s Ken’s round…)

Governance, Management, Administration

Governance

Management

Administration

IP Management

Group

Project

Governance Group

Programme Leader (PW)

Scion

•Financial Services

•Legal Services

•FRST interactions

•Project support

•HR

Science

Projects Large Datasets Polyploids Experimental “Project 4” eResearch QTL Mapping Design Portal

Science

Projects: Large Datasets

PolyploidsQTL Mapping

Experimental Design

“Project 4” eResearchPortal

Statisticians Rod Ball Rod Ball Rod Ball Rod Ball Mik Black

Ken Dodds Yi Lin Jia Ken Dodds Sharon Browning

Bernoit Auvary Nihal DeSilva Bernoit Auvary

Mik Black Mik Black

Geneticists David Chagne Gail Timmerman- Vaughan

Phillip Wilcox Gail Timmerman- Vaughan

Phillip Wilcox

John McCallum Mark McNeilage Rod Lea Paul Fisher

Phillip Wilcox Brent Barret David Chagne Geoff Gill

Paul Fisher PhD student David Chagne

PhD student