High Performance Computing for Healthcare (day 1)

12 July 2021 - 09:00-17:00
Will Furnass, Mark Dunning

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This workshop is being funded by the N8 Centre for Computationally-Intensive Research (N8 CIR), is being organised by the N8 CIR and TUOS and is being delivered by TUOS’ RSE team and TUOS’ Bioinformatics Core.


This workshop takes place over two days, 12 July and 14 July. Please only register if you will be able to attend both sessions if your application is successful.


High Performance Computing (HPC) is an increasingly important tool utilised by researchers, helping to overcome the limitations processing parallelism and memory found in even the most powerful desktop systems. With more computing power available researchers can perform more and bigger experiments leading to improved accuracy and better research outcomes. A further benefit is that HPC systems require researchers to define their workflow as jobs, which aids reproducibility.

However, making use of an HPC system, whether on-premise or in the cloud, isn’t as simple as just logging on and firing up the software. HPC users must be able to log in to remote computers using the bash shell, upload data and install software before they can begin to conduct experiments. Even the code may need to be adapted to run in parallel and maximise the benefits of HPC platforms.

For these reasons, many researchers shy away from adding HPC to their research toolkit.

This two-day workshop is intended to remove some of the mystery from HPC systems, making it easier for researchers to access them and accelerate their research. The material in this course will be healthcare-related using an omics data analysis. Participants will be given a set of sequencing reads from a next-generation sequencing experiment and perform the steps involved in identifying DNA mutations.

Although the example dataset used will be Genomics, many of the tools and techniques will be applicable to other healthcare use-cases.

Learning Outcomes

  • Improved familiarity with the bash shell
  • Install local software needed to access HPC (e.g. mobaxterm)
  • Transfer files to and from HPC
  • Submit, manage and evaluate the resource utilisation of HPC batch jobs
  • Be aware of the importance of parallelisation
  • Ability to run “embarrassingly parallel” Bioinformatics pipelines (e.g. quality control and alignment of a set of individuals profiled using next generation sequencing data)


  • Previous experience with the bash shell would be useful but the workshop does include an introduction to using the shell on HPC systems.
  • Some familiarity with biological concepts, including the structure of DNA, nucleotide abbreviations, and the concept of genomic variation within a population.


As part of the application process, you will be asked to provide a brief explanation of how attending this workshop will benefit your research. You may find it useful to write this piece before attempting to register for the event.

After the application deadline has passed, submissions will be considered, and successful applicants will be offered a place by e-mail. This process will help to ensure that each of the N8 universities are represented at, and benefit from the course.

This event is only open to those working or studying at one of the N8 Research Partnership universities. Please register using your academic (.ac.uk) e-mail address to help verify your eligibility.

The registration deadline is 5th July.

Contact Us

For queries relating to collaborating with the RSE team on projects: rse@sheffield.ac.uk

Information and access to JADE II and Bede.

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