Research

Grassroots Genomics

The Grassroots Genomics project at EI is a user-driven platform for integrating and reconciling wheat genomic information.

Project Summary.

Support: grasshelpdesk@earlham.ac.uk

Value: £2M

Grants:

BBS/E/T/000PR9783: Data access and analysis (Work Package 4 of Designing Future Wheat)

BB/N023420/1: Federating access to wheat data services for efficient genome-specific marker design

BB/L024144/1: CerealsDB: A community resource for wheat genomics

BB/M025519/1: Using field pathogenomics to study wheat yellow rust dispersal and population dynamics at a national and international scale

Integrative research requires extensive multi-level approaches to enrich and expose data and workflows so that informatics infrastructures can process them effectively. The Grassroots Genomics project represents EI’s contribution to the international Wheat Information System (WheatIS) to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots Genomics platform is powered by a powerful yet lightweight set of middleware services, called the Grassroots Infrastructure, which comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces.

The Grassroots infrastructure framework can be run locally or packaged in virtual containers and deployed on a variety of hardware thus representing a decentralised system, allowing information generators to retain control over their resources but allowing interconnected resources to access each other consistently. EI has an extensive National Capability in e-infrastructure to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots Genomics project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to EI provides community standardised methodologies for data integration, interpretation and discovery.

Impact statement.

In recent years, there has been a revolution in the generation of genomic data for cereal crops, especially wheat. Our goal is to engage the community of wheat researchers, from breeders to bioinformaticians, in generating, evaluating and integrating wheat data.

Grassroots Genomics aims to connect data generators and data users, providing an information-rich data sharing and analysis platform that will enhance the value of available wheat genomic resources.  We are committed to maintain and promote the principles of Open Data to enable discoveries and to enhance the value of integrative research, and work with wheat communities and technologists to deliver a coordinated and federated infrastructure.