Details of Award
NERC Reference : NE/Y003527/1
Metagenomics with High Performance Computing for environmental science
Training Grant Award
- Lead Supervisor:
- - E Rand, University of York, Biology
- Grant held at:
- University of York, Biology
- Science Area:
- Atmospheric
- Earth
- Freshwater
- Marine
- Terrestrial
- Overall Classification:
- Terrestrial
- ENRIs:
- Biodiversity
- Environmental Risks and Hazards
- Global Change
- Natural Resource Management
- Pollution and Waste
- Science Topics:
- Bioinformatics
- Environmental biotechnology
- Environmental Informatics
- High Performance Computing
- Tools for the biosciences
- Abstract:
- Microbial communities provide important environmental services and understanding them is essential for achieving net zero, tackling climate change, managing waste management and preventing the spread of antibacterial resistance. Sequencing entire communities using shotgun metagenomics is one of the most useful tools in creating this understanding. Metagenomics generates very large datasets which must be analyzed using High Performance Computers (HPC) using skills in which many environmental scientists are not trained. Such analyses require the installation of many different programs and databases creating a very, and often, impossibly, steep learning curve for the majority of environmental scientists. Assembling, polishing and binning metagenomes are computationally demanding and take many hours to complete which means that existing metagenomics courses typically focus on the downstream analyses such as taxonomic or community analysis or use the smaller amplicon sequence datasets for practical reasons. We will teach shotgun metagenomic analysis using an innovative combination of online sessions covering concepts and using live coding, offline time to allow very time-consuming steps to complete, and online drop-ins to support the offline time. Participants will be provided with cloud virtual machines configured with all the data and software so that they can first focus on the metagenomics pipeline without having to manage complex software installation. The course will be followed by two Code Retreats where participants can practice and get help applying the methods to their own data. Further support will be provided through weekly online drop-ins and Slack until the end of the project. This opportunity to revisit and apply training is a cornerstone of effective educational programmes but we are not aware of other research training courses that offer this. Additionally, we will train others in the automated management of AWS services to deliver Metagenomics and similar courses ("train the trainer") with materials and protocols we develop.
- NERC Reference:
- NE/Y003527/1
- Grant Stage:
- Completed
- Scheme:
- Doctoral Training
- Grant Status:
- Closed
- Programme:
- Advanced Training
This training grant award has a total value of £54,449
FDAB - Financial Details (Award breakdown by headings)
| Total - Other Costs |
|---|
| £54,449 |
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