Presentation 7 (PDF 1.5MB) - Wheat Initiative

wheatinitiative.org

Presentation 7 (PDF 1.5MB) - Wheat Initiative

Towards an Integrated

Wheat Information System

- Funding scenarios -

Mario Caccamo & Hadi Quesneville

Contributors : Takeshi Itoh, Paul Kersey, David

Marshall, Cesar Martinez, Dave Matthews, Klaus Mayer,

Franck Röber, Doreen Ware.


WheatIS Expert Working Group

Wheat Initiative steering

board commissioned a

WheatIS EWG

Expert Working

Group

interim chairs

M. Caccamo

H. Quesneville

• Build projects

• Build infrastructure

• Report to the

Wheat Initiative


WheatIS goals

Provide the wheat research community with a single entry

point of access to genetic and genomics resources.

Promote the development of services on top of

current wheat / Triticeae databases.

Authority to define guidelines for data curation,

nomenclature, standards and integration.

Registry for bioinformatics tools.


Project Principles

Build collectively to

better cope with

the needs of the

community

• Federated Network of Platform

• Ensure each platform sustainability through

promoting their visibility and adoption.

WheatIS will not replace the current wheat

databases

Incremental

implementation to

rapidly build an

operational site.

• Evolving infrastructure

• Rely on a distributed system.

• Use of Virtual Machine and Cloud

Computing technologies to share easily data and

tools.

Promote data

exchange following

an open-access

model.

WheatIS to support the adoption of standards

and the integration of data

• Gene nomenclature

• Best-practice guidelines


WheatIS Architecture

WheatIS core

File

repository

Web

portal

Search

Integrated

DB

Distributed Storage

Storage

Storage

Storage

DB

Indexes

WheatIS node

DB

Indexes

WheatIS node

DB

Indexes

WheatIS node


Work Packages

WP5: User interfaces,

outreach, training and

dissemination

WP1: Central data file

repository

WP2: Distributed index

search engine.

WP3: Data standards, data

management, and data

integration.

WP4: Data and Information

Infrastructure

WP6: Coordination and

project management.


Implementation: an iterative process

Step1 : Network building

Definition of standards

• define standards, nomenclature, formats,

etc.

• meta-data exchange

WheatIS

=

A web platform to

exchange data

Step2 : Integrated portal (virtual)

Search of data

• DBs federation

• Google-like search

WheatIS

=

A portal to access a

network of DBs

Step3 : Integrated DB

Integration of data

• In one place

• Focused on relevant data sets

• Consolidated and consistent

(Previous steps will provide a broad

view of available data)

WheatIS

=

An integrated DB


ICC & SC feedbacks on EWG plan

ICC & SC

Quicker

WheatIS

setup

Funding

Scenarios


Speed-up WheatIS

Implementation

Solutions available in a WheatIS node is

distributed to the other partners

Transparent for the end-users.

Necessitate the adoption by all

platforms of solutions provided by

others.

Facilitate other WheatIS nodes (not yet

identified) to join the initiative.


Funding Scenarios

Building and

maintenance of

the WheatIS

• Contributions of the partner WheatIS nodes

• Funding institutions dedicating resources to the

project.

• Additional resources will be looked for, from

national or international calls for proposals

Ressources

needed

• WP3, 5 and 6 could start with

no additional resources.

• WP1, 2 and 4 will require newly

recruited staff.


- Scenario 1 -

Additional staff recruited

in 2 leading WheatIS nodes in 2013

• TGAC (BBSRC, UK) and URGI (INRA, France) have already

partial solutions

‣ Distributed storage will be proposed between TGAC and URGI infrastructures.

‣ Funds available in May 2013, first WheatIS delivery for summer 2014.

• Pros:

‣ Quick start

‣ People used to collaborate

• Cons:

‣ Small community consultation

‣ Risk of lack of adoption

• Budget:

‣ One expert informatics engineer for TGAC and one for INRA for one year each.

Approximately 100,000 euros in addition to existing staff salaries.


- Scenario 2 -

Additional funds available immediately in

• Group of WheatIS nodes

several institutions

‣ Project could start from a collectively chosen solution.

‣ Funds available in May 2013, delivery of a first WheatIS in winter 2014.

• Pros:

‣ Larger collaborative work

‣ Better adoption by the WheatIS nodes

• Cons:

‣ Start is delayed from 6 months

• Budget:

‣ Probably at least one expert informatics engineer per node involved.

Approximately 50,000 euros per nodes for one year, in addition to

existing staff salaries.


- Scenario 3 -

No additional funds available

• Inventory all the partners willing to participate as a

WheatIS node

‣ Several projects will be written, coordinated and submitted independently

to fund specific tasks of the projects

‣ The start of the project would depend on the success of the calls for

proposals.

• Pros:

‣ Large collaborative network,

‣ Almost in its final configuration.

‣ No initial additional funds requested to the institutions.

‣ Best adoption configuration

• Cons:

‣ Start is delayed from at least 1 year


Budget summary

Additional salaries € Meetings Total €

Scenario 1 100,000 50,000 150,000

Scenario 2 50,000

x (wheatIS nodes involved

from the start)

50,000 50,000

+ (50,000 x nodes)

Scenario 3 0 50,000 50,000


Year1 Plan

• Organize the first annual meeting in 2013.

• Write a report describing the planned activities.

• Submit a research proposal to get funds for the

implementation of the WheatIS


Acknowledgements

Expert committee

Catherine Feuillet - INRA - France

Cesar Martinez - CIMMYT - International"

Dave Edwards - University of Queensland - Australia"

David Marshall - James Hutton Institute - UK"

Doreen Ware - Gramene - USA"

Eva Huala - TAIR - USA"

Hirokazu Handa - NIAS - Japan"

Jizeng Jia - CAAS - China"

Jorge Dubcovsky - UC Davis – USA"

Keith Edwards - University of Bristol – UK"

Klaus Mayer - MIPS – Germany"

Paul Kersey - EBI EMBL - International"

Peter Langridge - University of Adelaide - Australia

• Hélène Lucas (INRA)"

• Amanda Collis and Michael Ball (BBSRC)

More magazines by this user
Similar magazines