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 $NZ 938 K per annum  NERF  NZS portfolio  Viewed as important cross-sector underpinning capability

1. Background cont’d 5 year FRST-funded Oct 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 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 Establish project teams by March Establish HPC and data storage needs by June Establish eResearch portal by August Project 1 – Predicting phenotype from ‘Large Data Sets’ – complete June Project 2 – ‘Polyploid’ QTL mapping – complete by end of Project 3 – Innovative Experimental designs – January 2009 – Sep Project 4a – Project analysis Oct 2010 – Janu Project 4b – Method development and implementation Feb Sept

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 ScienceScience 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 Ball Ken Dodds Bernoit Auvary Mik Black Phillip Wilcox Rod Lea David Chagne PhD 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 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 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 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 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 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 Polyploids QTL Mapping Experimental Design “Project 4”eResearch Portal StatisticiansRod Ball Mik Black Ken DoddsYi Lin JiaKen DoddsSharon Browning Bernoit AuvaryNihal DeSilvaBernoit Auvary Mik Black GeneticistsDavid ChagneGail Timmerman- Vaughan Phillip WilcoxGail Timmerman- Vaughan Phillip Wilcox John McCallumMark McNeilageRod LeaPaul Fisher Phillip WilcoxBrent BarretDavid ChagneGeoff Gill Paul FisherPhD studentDavid Chagne PhD student