A High-Performance Computing (HPC) platform that will increase the pace of crop science and climate change research has been established by six leading UK research organisations.
The new HPC cluster is dedicated to the study of crop genetic diversity. It will enable crop researchers to share data, develop new methods of analysis and deliver training, and act as the basis for establishing new collaborative programmes of innovative science. Within the partner organisations alone, the bioinformatics resource will support the work of more than 400 scientists including early career researchers and PhD students.
Funded by the Biotechnology and Biological Sciences Research Council, and with support from the Scottish Government, the project has been led by the crop research organisation NIAB, in partnership with the James Hutton Institute, the Royal Botanic Gardens Kew, Scotland’s Rural College, the Royal Botanical Garden Edinburgh and the Natural History Museum. The platform includes over 1,700 CPU cores, 15 terabytes of memory and 1.5 petabytes of storage capacity. It will be hosted at the James Hutton Institute’s Aberdeen campus.
Project leader, NIAB’s Professor Mario Caccamo, explains that the HPC cluster will support and expand the work of the entire consortium and their extensive network of collaborators around the world.
“Developments in sequencing and genotyping technologies, together with advances in environmental monitoring and characterisation, are leading to rapid changes in the opportunities that are available to evaluate and utilise genetic diversity in crop plants and their wild relatives, in response to climate change and other global food and farming challenges,” says Professor Caccamo.
Professor Colin Campbell, Chief Executive of the James Hutton Institute, adds: “High-performance computing is central to so many areas of science performed by the Institute. It allows us to tackle data analysis problems at scales beyond those possible with normal PCs, such as processing genetic sequencing, environmental and remote sensing data sets, analysing hyperspectral images of plants, or running complex climate and weather models.
“Our Research Computing group has over 16 years’ experience in providing HPC facilities, and we are really excited by this expansion of resource and the enablement of remote access to the other partners – particularly during this difficult time with so many staff working from home.”
Professor Caccamo highlights that a major factor in developing the research infrastructure to support and nurture such activities was the provision of access to suitable computational resources.
“The new platform is primarily focused on supporting our work on the characterisation and utilisation of novel genetic diversity, for both the improvement of current agricultural and horticultural crops as well as the breeding of new varieties. Access to advanced bioinformatics and data analysis tools will enable us to manage, model and mine vast amounts of genomic data to identify genetic markers and traits that provide the key to better varieties and new crops,” finishes Professor Caccamo.
Crop Diversity Bioinformatics HPC Resource
The funding for this project included the BBSRC 18ALERT grant - BB/S019669/1. More information is available at www.cropdiversity.ac.uk