# Scaling Gene Regulatory Networks Simulations¶

## Prerequisites¶

• 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 🤦

## Content¶

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

Lesson Overview
General overview of Simulations , Gene Regulatory Networks and Simulating Gene Regulatory networks
Describe how sismonr package works and running the first simulation
Introduction to High Performance Computing
Introduction to HPC Job Schedulers, Slurm Scheduler & life cycle of a Slurm job, Assessing resource utilisation and profiling
Introduction to specifications in Parallel Computing, Slurm Job arrays and Exercises on Scaling networks
Interpreting sismonr output and Visualising the simlulations

## Schedule¶

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