Parameter inference for stochastic reaction models of ion channel gating from whole-cell voltage-clamp data

Code to replicate the analyses from the article "Parameter inference for stochastic reaction models of ion channel gating from whole-cell voltage-clamp data".

Figures 3-12 of the paper can be reproduced by running the corresponding .sh files fig3.sh, fig4.sh, etc. The figures will be stored in the folder "./results/allFigures/", which will be dynamically generated after running the code.

Code dependencies:

R version: 4.2.1-foss-2022a

Packages:
spsUtil_0.2.2
pracma_2.4.2
stringr_1.5.0
nloptr_2.0.3
tmvtnorm_1.5
gmm_1.8
sandwich_3.0-2
mvtnorm_1.2-1
Matrix_1.5-1
deSolve_1.35
Deriv_4.1.3

Please note: the required packages will be automatically installed when running the code. To allow for this, a CRAN repository must be set first, by including the line

options(repos=c(CRAN="URL_OF_REPOSITORY"))

to the .Rprofile, located in the user home directory.