Now collecting expressions of interest (EOIs): Scaling-up Gene Regulatory Network Simulations (online)

We are now collecting expressions of interest (EOI) for the online workshop advertised below. Please note that, due to limited resources, not everyone who fills out an EOI will get a seat at this workshop.  Expressions of interest will close on Tuesday 9 November.

Click here to fill out an expression of interest

This workshop has been jointly developed by Olivia Angelin-Bonnet, lecturer in Applied Statistics at Massey University, NeSI, and Genomics Aotearoa.  Olivia researches how to decipher genotype-phenotype interactions through regulatory networks using omics datasets, and will speak about simulating gene regulatory networks, using R and Julia.  Specifically, Olivia and Dini will explain to attendees:

  • Why simulations are valuable in systems biology,
  • What regulatory networks are and how they can be modelled,
  • How to use the sismonr R package to simulate a small regulatory network, and
  • Introduction to High performance computing (HPC) 
    • HPC architectures
    • Batch systems and using a Slurm scheduler 
  • How to scale up simulations on a HPC through profiling and optimization

For more information about simulating gene regulatory networks with the sismonr package, refer to this webinar Olivia presented on the topic in 2020:

Who is this workshop for

It is preferred (but not required) that attendees of this workshop have some knowledge of molecular biology, in particular gene expression and regulation.  This workshop is a great introduction to how modelling and simulations can help answer important biological questions, and why high performance computing is essential for scaling up simulation-based projects.

Recommended knowledge and prerequisites

  • Required: Introductory command line skills
  • Strongly recommended: Familiarity with R functions and packages.  If you are not familiar with R we ask you to review this material (
  • Preferred: Basic molecular biology knowledge (gene expression and regulation) preferred

If you are concerned about any of the prerequisites above feel free to email and we can help you determine if this workshop is a good fit for you


This is a fully online, hands-on workshop. If you are selected to attend we will be in touch with instructions.  Selected attendees will be required to attend a 30 minute setup session, date and time tbd.

Instructors/ helpers:

  • Olivia Angelin-Bonnet (Massey University)
  • Dinindu Senanayake ( New Zealand eScience Infrastructure)
  • Ngoni Faya (Genomics Aotearoa) 
  • Matthieu Vignes (Massey University)
  • Matt Bixley ( New Zealand eScience Infrastructure)

Note: The event times listed below are in NZDT 

Event Date: 
Wednesday, December 1, 2021 - 10:00 to Thursday, December 2, 2021 - 16:00