HPC

Analysis of big data sets often breaks down on your laptop: it’s too slow, it’s too heavy, your computer does not have enough memory… In that case the Vlaamse SuperComputer will come to the rescue.

The course shows how to use the VSC at KULeuven (but we explain the differences with Gent) for data analysis. We start with a simple example (BLASTing sequences) to show you how to run scripts on the VSC. In the afternoon we’ll use a more challenging example: analysis of a spatial transcriptomics dataset.

Morning

• Slides on doing HPC on the VSC
• Tutorial on getting access to the VSC (html file – open in browser)
• Tutorial on logging on to the VSC (html file – open in browser)
• Tutorial on using Open OnDemand
• Tutorial on using software on the VSC (html file – open in browser)
• Tutorial on running scripts on the VSC (html file – open in browser)
• environment.yml file for setting up the conda environment
• sequence database for BLAST exercises
• sequence for first BLAST exercise
• sequence1 for next BLAST exercises
• sequence2 for next BLAST exercises
• sequence3 for next BLAST exercises
• sequence4 for next BLAST exercises
• fasta file with the 4 sequences for the multithreading BLAST exercise

Afternoon

• on $VSC_DATA run: git clone https://github.com/vibspatial/targeted_transcriptomics_training.git
• install miniconda on $VSC_DATA: check Tutorial on using software on the VSC of the morning session
  ! don’t forget to export the path of the miniconda3 to $PATH