Integrated Breeding Platform 2 nd Annual Meeting, Wageningen, June 1-3, 2011 Jean-Marcel Ribaut GCP, Mexico

Integrated Breeding Platform Breeding Services Support Services Configurable Breeding Workflow System Cyber Infrastructure Custom Formatted Data Files Local Database Web Service Data Source High Performance Computer Information System Portal SoapLab MOBY, 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 selection Crossing Population development Germplasm Management Open Project Specify objectives Identify team Data resources Define strategy Project Planning Experimental Design Fieldbook production Data collection Data loading Germplasm Evaluation Marker selection Fingerprinting Genotyping Data loading Molecular Analysis Quality Assurance Trait analysis Genetic Analysis QTL Analysis Index Analysis Data Analysis Selected lines Recombines Recombination plans Breeding Decisions Administration Project conf. Workbench administration & configuration Breeding Management System Trial Fieldbook Environment characterization system Field Trial Management System Genotypic Data Management System Sample management Analytical Tools Sel. Indices Breeding App. MARS App. Cross Prediction Simulation Decision Support Tools Breeding ApplicationsAnalytical Pipeline Breeding mana. Genealogy mana. Query tools Sample mana. Data management Statistical analysis Molecular Genetic

Tool and CWS Development a6b 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 6c Stand-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 VSNi Development 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 Bases Phenotypic DB ♦ICIS Schema ♦New GUI ♦Not everybody needs to know about all the functionalities Genotyping DB ♦Builds on the ICRISAT Crop Resources Information System ♦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 Private DB Users CGIAR Crop Lead Center Capacity building Portal

Sustainable Data Management IBP 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!