Synthetic Models for Stochastic Biochemical Reaction Systems

This repository contains the code for the paper

K. Öcal, Michael U. Gutmann, G. Sanguinetti, R. Grima, "Inference and uncertainty quantification for stochastic gene expression via synthetic models", https://doi.org/10.1101/2022.01.25.477666

Dependencies include:

• Catalyst.jl
• FiniteStateProjection.jl
• MomentClosure.jl
• GpABC.jl
• BlackBoxOptim.jl

This repository contains a fork of HMMBase.jl (found here) to support time-inhomogeneous HMMs. Running the MAPK Pathway example requires data from [1] which can be obtained from the authors.

Examples:

• Autoregulatory Feedback Loop (folder afl)
• Genetic Toggle Switch (folder ts)
• MAPK Pathway (folder hog1p)

Please do not hesitate to get in touch if you have questions about the code or the paper.

References:

[1] G. Neuert, B. Munsky et al., "Systematic identification of signal-activated stochastic gene regulation", Science 339 (2013). https://doi.org/10.1126/science.1231456