HPC 6: HPC for Life Sciences and Bioinformatics

Course content

The purpose of this one-day workshop is intended to introduce Biologists, Chemists and Bioinformaticians to the High Performance Computing facilities at Leeds.

Although it will include material from some other workshops (particularly HPC 1: Introduction to High Performance Computing at Leeds), it’s main purpose is to introduce the range of HPC services at Leeds, how they can be used in Life Sciences research with a specific emphasis on NextGen Sequence analysis.

We will cover:

  • Basic command-line Linux
  • Using HPC for large-scale computing
  • Choosing and installing codes and applications
  • Running codes and applications through the batch scheduler
  • Data storage and management
  • Visualising data in R and Python
  • Life science and Bioinformatics software and libraries (using R and Python)
  • Automating analysis pipelines using the command-line shell and Snakemake

Prerequisites

This is a hands-on workshop and is intended for High Performance Computing “novices” and advanced skills are NOT required.

A working knowledge of Unix is helpful but not necessary; we don’t expect that you already have experience using HPC.

Duration

1 day

Frequency

This workshop usually runs twice each academic year

Suitability

All research staff and students

Booking

This workshop is booked through the IT Training Unit