Scaling-up Gene Regulatory Network Simulations
with an introduction to parallelisation and High Performance Computing
Author(s)
Olivia Angelin-Bonnet, Dinindu Senanayake
Excerpt
2-days workshop offering an introduction to the stochastic simulation of Gene Regulatory Networks using the R package sismonr, and to scaling up simulations on a high-performance computer.
Date
December 1 – 2, 2021
Location
Online
Event
Abstract
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
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: https://datacarpentry.org/R-genomics/01-intro-to-R.html
- Preferred: Basic molecular biology knowledge (gene expression and regulation) preferred