Integrated Breeding Platform

2nd Annual Meeting, Wageningen, June 1-3, 2011

Jean-Marcel Ribaut GCP, Mexico

Integrated Breeding Platform

Breeding Services

SupportServices

Ser

vice

s

Configurable Breeding Workflow System

Cyber Infrastructure

CustomFormatted

DataFiles

Local Database

Web ServiceData Source

HighPerformance

Computer

Info

rmat

ion

Sys

tem

Por

tal

SoapLabMOBY, GDPC, BioCase/TAPIR

Data Sources

Our Most Challenging Initiative: The Context Everybody needs it (and needs it right now!) Everybody has an opinion on what it should

look like IBP competes/builds on:

A degree of valuable assets Certain cherished practices

IBP competes/overlaps with: Ongoing initiatives Ideas never implemented

Broad diversity of the potential users Different expectations and needs Different view points on workplan priorities

Potential conflict of interest at different levels

Our Most Challenging Initiative:The real Challenge It is not really about the tools or the technology It is about changing people’s behavior:

How they think How they do things Ways to share things

Moving from individual to corporate thinking

IBP should address the technical issue IBP can help with some behaviour change Support from institutional upper management a

must to succeed Need to learn from the Private Sector

It is GCP’s responsibility to manage that level of complexity

One size does not fit all

The IBP will not solve all your institutional problems

IBP must offer options and alternatives for tools and services

There is a need to focus and prioritize activities

Evolution in the IBP Approaches ♦ Management

♦ More proactive management by GCP♦ Creation of an implementation committee ♦ More robust communication strategy

♦ Organisation

♦ Shift from functionality to breeding applications♦ Implementation of Configurable Workflow System (CWS) supported by

an Integrated Breeding workbench♦ Rethink and reorganise the coding and software development effort

♦ New alliance

♦ CWS to be ‘plugged’ into the iPlant cyber Infrastructure♦ Access to GenStat tools and support

♦ Hard decision

♦ The development of the GCP middleware has been interrupted♦ Some elements of the domain model have been redeployed

AA

The IBP Configurable Breeding Workflow System

Breeding Activities

Parental selectionCrossingPopulation development

GermplasmManagement

Open ProjectSpecify objectivesIdentify teamData resourcesDefine strategy

Project Planning

Experimental DesignFieldbook productionData collectionData loading

GermplasmEvaluation

Marker selectionFingerprintingGenotypingData loading

MolecularAnalysis

Quality AssuranceTrait analysisGenetic AnalysisQTL AnalysisIndex Analysis

DataAnalysis

Selected linesRecombinesRecombination plans

BreedingDecisions

AdministrationProject conf.

Workbenchadministration

&configuration

Breeding Management

System

Trial FieldbookEnvironment characterizationsystem

Field Trial Management

System

GenotypicDataManagementSystem

Sample management

Analytical Tools

Sel. IndicesBreeding App.MARS App.Cross PredictionSimulation

Decision Support Tools

Breeding Applications Analytical Pipeline

Breeding mana.Genealogy mana.Query tools Sample mana.

Data managementStatistical analysisMolecular Genetic

Tool and CWS Development

12345

6a 6b

Basic mock-up (MU) Stages 2&3 iteration (3–4weeks)

Functional MU: α & β prototypes

Downloadable CWS(Java, middleware)

Documentation of the structure and functionality of the tool

Graphical representation of the tool workflow annotated flow diagrams

Development of corresponding algorithms to run the analysis

Web-based CWS iPlant Cyber-infrastructure

User interactions

6cStand-alone Tools

(Java, C ++, etc, FlapJack)

Coordination parameters for the user interface

June 2011 June 2012 June 2013

The Users

Not all IBP users need to access the latest technologies ♦ Needs for:

♦ Research tasks♦ Routine tasks

♦ Research users:♦ Are research and application-oriented♦ Need to access research and routine tools♦ Should be ready to pay for specific service♦ Should be ready to go through sharp learning curve to access new

technologies

♦ Applied users: ♦ Have applied objectives focusing on limited number of applications♦ Need to access simple analytical pipeline/tools to be used on a routine basis♦ Are not ready to spend a lot of time to learn how to use new tools

Although IBP supports the development of research tools, the primary goal of the Platform is to serve the needs of users in applied research

Salient IBP Principles♦ CWS tools must be:

♦ Simple (not easy to define in the IBP context!)♦ A simple interface that can run on the most suitable models and

algorithms♦ Able to serve 80% of the needs of our users (in the short term)♦ Unafraid of being ‘paternalistic’ (highly structured)

♦ Robust and reliable♦ Have an efficient support service in place

♦ Flexible♦ Downloadable or can be run on the web♦ Easy to modify and upgrade

♦ Freely accessible to breeders in R4D♦ Does not mean that nobody is paying for it

♦ Hooked to public DBs♦ Data publication and sharing is absolutely critical

We should explore alliances with the private sector

PPP: Collaboration with VSNiDevelopment of a Breeding View♦ BV targets routine MB analysis♦ A simple interface that can run on the most advanced algorithms♦ Advanced users can access the full version of GenStat♦ During the development of BV the 14 user cases will access

GenStat

PPP: an attractive and sustainable approach?♦ Builds on already-established commercial product ♦ VSNi to ensure the maintenance and support service♦ No direct competition with the flagship product of GenStat, so it will

be possible to have commercial flexibility,♦ Corporate fee to support access and maintenance♦ Free for people who are ready to release their data♦ Discount for IBP users, etc

There is no free meal!

A model to explore further the sustainability of the IBP tools

Data BasesPhenotypic DB

♦ ICIS Schema♦ New GUI♦ Not everybody needs to know about all the functionalities

Genotyping DB♦ Builds on the ICRISAT Crop Resources Information System

http://icris.icrisat.org/ICRIS/ ♦ Already quite a good user interface based on feedback from

users

Other features♦ The best option for the IBP in the short term is to work with these DBs♦ IBP is aware of and follows the progress of:

♦ Germinate; Maize DB; KDDart

♦ Readiness to move to the new DB generation when superiority proven

♦ Support the transfer of GMS and DMS if necessary

Data Storage and Publication

Web

Local

• Data documentation

• Data curation

• Data publication

Central DB

Central DB

Private DB

Users

CGIAR Crop Lead Center

• Capacity building

Portal

Sustainable Data ManagementIBP creates a unique opportunity for GCP to play a

catalytic role in data management at the CG level

Crop Lead Centres (CLCs) will be responsible for

establishing standard technology for breeding their mandate

crop(s), and they will also be resource centres for

information and technology for outside users breeding these

crops. ToRs: clear rights and obligations

Allocate space in respective crop databases to store and publish

relevant data generated through the platform – including data from

outside their Centre – for crop(s) under the Centre’s leadership

Still under discussion

Conclusion and Perspectives

Challenges and Opportunities

Develop or adjust suitable tools, services and an information system to meet most of the IBP users’ needs in a dynamic and competitive environment

The IBP will provide alternatives and does not need to address all the issues; it will have the flexibility to adjust, but only when superiority has been proven

Training and capacity building on IT and new technologies The IBP can rely on and use novel approaches and services

E-learning, KIM tools, outsource some training components Data access, quality control and documentation The right time to push for a change in the CG system

CGIAR reform Resources in proposal for data management

Conclusions

¨ More then ever a learning-by-doing initiative¨ Revised plans based on lessons learnt from year one¨ A lot has been achieved in year two:

¨ A solid workplan for the coming years developed¨ A beta version available for critical tools of the WS¨ 9 DBs implemented with respective trait dictionary and templates ¨ Local infrastructure implemented at several sites¨ Important collaborations established¨ A web portal initiated ¨ Establishment of CoPs initiated

A big thanks to all the different IBP collaborators and partners who have been working very hard during the second year

Thank you very much!