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Delayed-SSA-Models

This code allows one to simulate the delayed stochastic simulation algorithm (DSSA) for the mechanistic and delayed-telegraph models of gene expression in https://www.biorxiv.org/content/10.1101/2021.06.08.447592v1.abstract. Descriptions of each file are provided below.

  • DSSA-Mech.jl: Julia code that allows one to simulate the mechanstic model in Eq. (1).
  • DSSA-delayed-telegraph.jl: Julia code that allows one to simulate the delayed telegraph model in Eq. (2).
  • Example-SSA-mechanistic.ipynb: Exhibits usage of the DSSA code from DSSA-Mech.jl.
  • Example-SSA-delayed-telegraph.ipynb: Exhibits usage of the DSSA code from DSSA-delayed-telegraph.jl.

The DSSA here utilises Algorithm 2 of Barrio, Manuel, et al. "Oscillatory regulation of Hes1: discrete stochastic delay modelling and simulation." PLoS computational biology 2.9 (2006): e117.

For queries on the code above please contact james.holehouse@ed.ac.uk or jamesholehouse1@gmail.com. For non-code related queries please contact ramon.grima@ed.ac.uk.