Transcript Virtual Institute of Statistical Genetics - MapNet

VISG Session 2009
Phillip 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 09
1.2 Establish project teams by March 30 2009
1.3 Establish HPC and data storage needs by June 30 2009
1.4 Establish eResearch portal by August 30 2010
1.5 Project 1 – Predicting phenotype from ‘Large Data Sets’ –
complete June 30 2012
1.6 Project 2 – ‘Polyploid’ QTL mapping – complete by end of 2011
1.7 Project 3 – Innovative Experimental designs – January 2009 –
Sep 30 2013
1.8 Project 4a – Project analysis Oct 2010 – Janu 2011
1.9 Project 4b – Method development and implementation Feb
2011- Sept 30 2013
2. VISG Structure
IP
Management
Governance
Project
Governance
Group
Group*
Scion
•Financial Services
•Legal Services
Management
Programme Leader
(PW)
Administration
•FRST interactions
•Project support
•HR
Projects
S
c
i
e
n
c
e
Statisticians
Polyploids
Experimental
QTL Mapping
Design
Rod Ball
Rod Ball
Sharon Browning
Ken Dodds
Yi Lin Jia
Bernoit Auvray
Nihal DeSilva
Rod Ball
Ken Dodds
Bernoit Auvary
Mik Black
Phillip Wilcox
Rod Lea
David Chagne
PhD student
Gail Timmerman –
Vaughan
Large Datasets
“Project 4”
eResearch
Portal
Mik Black
Rod Ball
Mik Black
Geneticists
David Chagne
John McCallum
Gail TimmermanVaugh
Phillip Wilcox
Mark McNeilage
Paul Fisher
Brent Barret
Paul Fisher
Geoff Gill
David Chagne
PhD student
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 Governance
Roles
 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
IP Management
Project
Group
Governance Group
Scion
Governance
•Financial Services
Management
•Legal Services
Programme Leader
(PW)
Administration
•FRST interactions
•Project support
•HR
Projects
Large Datasets
Polyploids
Experimental
QTL Mapping
Design
Science
“Project 4”
eResearch
Portal
Science
Projects:
Statisticians
Large
Datasets
Polyploids
QTL Mapping
“Project 4”
Rod Ball
Rod Ball
Rod Ball
Rod Ball
Ken Dodds
Yi Lin Jia
Ken Dodds
Sharon Browning
Bernoit Auvary
Nihal DeSilva
Bernoit Auvary
Mik Black
Geneticists
Experimental
Design
Mik Black
Mik Black
David Chagne
Gail TimmermanVaughan
Phillip Wilcox
Gail TimmermanVaughan
John McCallum
Mark McNeilage
Rod Lea
Paul Fisher
Phillip Wilcox
Brent Barret
David Chagne
Geoff Gill
PhD student
David Chagne
Paul Fisher
eResearch
Portal
PhD student
Phillip Wilcox