Cloud resources for Designing Future Wheat

Designing Future Wheat is a UK-wide, cross-Institute large strategic grant from BBSRC awarded to eight UK institutions to undertake and improve access to wheat research. Part of this project is work package 4, Data Access and Analysis, which aims to deliver cutting-edge wheat data to the community as soon as possible after generation, and made available under open access policies, e.g. Toronto. This requires advances in and development of efficient and easy-to-use data infrastructure. Whilst DFW funds the development of the software aspects for data management, computational hardware was also required to allow the storage and use of DFW data. Rob Davey (EI) and Chris Rawlings (RRes), DFW WP4 leads, were successful in applying for a BBSRC 16ALERT mid-range equipment grant to uplift the cloud infrastructure already provided through the CyVerse UK project.
As such, we can now offer a safe, secure, and reproducible cloud environment to DFW researchers, for free, to undertake analyses as part of the DFW project. Users can request virtual machines within the CyVerse UK cloud with a variety of configurations, including storage, CPU and memory options to fulfil their needs. These machines can be pre-populated with reference wheat datasets, and you can upload your own data. These machines are well suited to typical bioinformatics tasks:
  • sequence data quality assessments and filtering
  • RNA-seq / transcriptomics / gene expression analysis
  • variant calling
  • phylogenetics
Machines can also be preconfigured to run Galaxy, RStudio, and Jupyter Notebooks, and come with secure shell (SSH) access via public key as standard. You can also transfer data to and from the main CyVerse Data Store and Data Commons. In the near future, we will also be providing large memory virtual machines to allow researchers to undertake genome and pan-genome assembly, as well as graph-based assembly interrogation through variant graphs, and virtual desktop functionality so users will be able to run desktop applications such as IGV or Flapjack. If you are a DFW-funded researcher please contact us to let us know your requirements and to request a VM. If you are a commercial breeder/researcher and would like to gain access to these resources, please contact us to discuss pricing. If you are a BBSRC-funded researcher, you can still gain access to CyVerse UK resources as part of Earlham Institute’s National Capability. Please contact us for options.