Software


A tutorial by James Holehouse on running the SSA and FSP in Julia applied to genetic auto-regulation. Also, gives a short review of parameter inference using maximum likelihood approach and Bayesian methods. https://github.com/jamesholehouse/SSAandFSPexample
 

MomentClosure.jl

MomentClosure.jl is a Julia package by Augustinas Sukys providing automated derivation of the time-evolution equations of the moments of molecule numbers for virtually any chemical reaction network using a wide range of moment closure approximations. Source code and documentation are available at https://github.com/augustinas1/MomentClosure.jl. Paper briefly discussing the package PDF

FiniteStateProjection.jl

FiniteStateProjection.jl is a Julia package by Kaan Öcal providing the Finite State Projection algorithm for the efficient simulation of stochatsic chemical reaction networks. Source code and documentation are available at https://github.com/kaandocal/FiniteStateProjection.jl

DelaySSAToolkit.jl

DelaySSAToolkit.jl is a Julia package by Xiaoming Fu for modelling reaction systems with non-Markovian dynamics, specifically those with time delays. Source code and documentation are available at https://github.com/palmtree2013/DelaySSAToolkit.jl. Paper briefly discussing the package PDF

Neural Estimation of Stochastic Simulations for Inference and Exploration (NESSIE)
Nessie leverages the representational power of neural networks to approximate the solutions of the chemical master equation. Source code and documentation (by Augustinas Sukys and Kaan Öcal) are available at https://github.com/augustinas1/Nessie Paper introducing and showing the power of NESSIE PDF