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Scaling Gene Regulatory Networks Simulations



  • Familiarity with bash and R
  • Basic molecular biology knowledge preferred (gene expression and regulation)
  • HPC knowledge preferred

Learning objectives

By the end of this workshop, participants should be able to:

  • explain the concept of modelling and simulations, and how simulations can help answer research questions;
  • briefly describe the main steps of gene expression, and explain what is a Gene Regulatory Network;
  • list several classes of GRN models;
  • generate a small random GRN with the sismonr package and simulate the expression of its gene;
  • submit and manage jobs on a cluster using a scheduler and use software through environment modules;
  • automate a large number of tasks on a HPC using array jobs.

Some of the things we won't cover in this workshop 🙅

  • How to :
    • construct a mathematical or statistical model for a specific biological system of interest;
    • estimate model parameters based on experimental data;
    • reconstruct a GRN from experimental data;
  • Any questions we don't have an answer for 🤦


Before getting started, have a look at the Supplementary data for instructions on how to connect to NeSI Mahuika Jupyter.

Lesson Overview
1. Introduction General overview of Simulations , Gene Regulatory Networks and Simulating Gene Regulatory networks
2. Getting started with sismonr Describe how sismonr package works and running the first simulation
3. Scaling up your work Introduction to High Performance Computing
4. Working with job scheduler Introduction to HPC Job Schedulers, Slurm Scheduler & life cycle of a Slurm job, Assessing resource utilisation and profiling
5. Parallel job arrays Introduction to specifications in Parallel Computing, Slurm Job arrays and Exercises on Scaling networks
6. Post-processing Interpreting sismonr output and Visualising the simlulations


Day Time Topic
1st day: 10am-12:30pm 1. Introduction
12:30pm-1:30pm Lunch break
1:30pm-2:30pm 2. Getting started with sismonr
2:30pm-3.30pm 3. Scaling up your work
4. Working with job scheduler
2nd day: 10am-12pm 5. Automating large number of tasks
12pm-1pm Lunch break
1pm-2.30pm 5. Post-processing
2.30pm - Question time