Angelin-Bonnet, Olivia

How R and Julia hang out together to simulate complex biochemical interaction networks

Institute of Fundamental Sciences, Massey University

Simulating the expression of genes and the interactions between their products using computational models is a challenging task. For a simulation to be representative of the biological complexity, one must build complex mathematical models to represent the system behaviour. Under a stochastic framework, simulating the system state over time amounts to computing the sequence of biochemical reactions occurring at each time step. This is achieved using a stochastic simulation algorithm, and results in long computational running time. In order to fasten up the computation, we decided to use the programming language Julia to run such simulations. During this talk I will be presenting the concept of expression data simulation algorithm, and explain how we used the R package XRJulia to call Julia functions from within R.

This presentation is eligible for the NZSA Student Prize.