In an era of cheaper and faster sequencing, genomics can mean having to find a needle-sized piece of vital information in a haystack-sized wealth of data. Our Grassroots tool helps you sort the wheat from the chaff.
Challenges for researchers have shifted. Datasets are much larger and more complex than ever before and biologists are now working with an unprecedented level of detail.
While science sometimes still means the laborious search for scarce data, the rise of high-throughput technologies means scientists often find themselves sifting through large amounts of data they don’t need, to find the small amount which is relevant to their project.
At the Earlham Institute, we develop tools that help researchers share, access, and use those large datasets effectively.
And one of those tools is Grassroots Genomics - an open-source platform supporting the sharing of plant genomic data. Simon Tyrrell, Research Software Engineer, leads the programme at the Earlham Institute.
“Grassroots is an open-source platform intended for plant biologists to share data and resources. There are a variety of sources - at the moment, data comes primarily from wheat but we’ve also recently begun offering data on legumes,” he says.
“It would be usable to track and share data from any crop.”
Grassroots allows researchers to upload and analyse field trial data - including images - using mobile apps. Uploads can be conducted in real time, improving data collection accuracy. The platform is a one-stop-shop for bioinformatics tools and offers services like nucleotide searches, pathogen genomics, and metagenomic analysis.
A valuable function of Grassroots is the ability to search field trial data, including heat maps, plots, and related metadata.
Efficient sharing of data has clear benefits.
The right tools and platforms allow researchers to share, access and use diverse datasets - improving research outputs, collaboration, and reproducibility while reducing time spent on unnecessary duplication of work.
And sharing can have real-world effects on large, complex issues. The difficult problem of feeding the global population during the climate crisis could be enhanced by pooling data and resources.
Programmes such as Grassroots also allow for standardisation and easy searchability. FAIR data – which stands for findable, accessible, interoperable, and reusable – is a cornerstone of modern biology.
“When I began working on wheat field trials, we used physical data in book form which was hard to search and lacked coherence. Data from Grassroots is searchable, viewable on the internet, and exportable,” says Simon.
He explains the data can be broken down to view as a researcher needs it, including into statistics and visual heat maps of fields.
“For example, if you wanted to breed for taller wheat, Grassroots can provide you with a heat map which would match taller growth to particular seeds or applied treatments,” he says.
We already have a good amount of data being uploaded, but - like any data-sharing platform - Grassroots will only get even better and more detailed as more people sign up and start uploading their trials and results.
Grassroots began development in 2014, as part of WISP (the Wheat Improvement Strategic Programme), a Biotechnology and Biological Sciences Research Council (BBSRC)-funded collaborative programme.
At that time, it was used to track and share research into yellow rust and stem rust, both serious pathogens of wheat.
However, it became clear the platform could have wider applications and about five years ago it began offering general data from field trials.
Services now available to users include browsing field trial data, exploring pathogenomics, searching nucleotide or protein queries, and submitting images and data from the field.
Grassroots is currently contributing to the BBSRC-funded cross-institute Delivering Sustainable Wheat programme. It has been developed in collaboration with Rothamsted Research, the University of Bristol, the John Innes Centre (JIC) and the National Institute for Agricultural Botany (NIAB).
“We already have a good amount of data being uploaded, but - like any data-sharing platform - Grassroots will only get even better and more detailed as more people sign up and start uploading their trials and results,” Simon says.
“I’d encourage anyone with an interest in crop genomics to consider it as an option.”
Grassroots is available as an online portal and as an app. The project is fully open source and the source code is available on GitHub.
For more information on getting Grassroots, and citing the project if you are using it, please visit our webpage.
