Synthetic data studies for hERG kinetics at room temperature.
To reproduce the results in the supporting materials in the publication, run the scripts in the order as listed.
Above libraries should be installed/included in ../lib/.
- fit.py: Simple fitting for a cell;
Usage: python fit.py [int:cell_id] --optional [N_repeats] - fit.sh: Bash script calling fit.py as batches
- mcmc.py: Run MCMC for one cell, usage:
python mcmc.py [cell-id] - mcmc.sh: Bash script to run MCMC for multiple cells by calling mcmc.py
- hbm.py: Run hierarchical Bayesian model (HBM) using Metropolis-Within-Gibbs (MWG)
- pseudohbm.py: Run HBM using pseudo-MWG, requires individual cells' MCMC chain, and plot results
- plot-single-mcmc.py: Plot single MCMC result as marginal histograms and traces
- plot-pseudohbm-cov.py: Plot pseudo-MWG covariance results against true values
- plot-hbm-v-pseudohbm.py: Plot HBM results inferred using full MWG versus pseudo-MWG
- plot-hbm-v-pseudo2hbm.py: Plot HBM results inferred using full MWG versus simplified pseudo-MWG
- pseudohbm-convergence.py: Plot HBM pseudo-MWG convergence to true values
- pseudo2hbm-convergence.py: Plot HBM simplified pseudo-MWG convergence to true values