herg-real-data

Application to real hERG data

All results are cached, so all figures can be re-generated by simply running the figure plots. All results for Hypothesis 2 can be reproduced by running:

1. Run fit-fix-kinetics-simvclinleak.sh to get initial guesses for the artefact parameters.
2. Run fit-simvclinleak-scheme3-parallel.py to run fits with Eq. (4.14) using Algorithm S1.
3. Run compute-rmsd-hist-fix-kinetics-simvclinleak-scheme3.py to compute all the RRMSE values.

Figure 7, Table S4: Run plot-rmsd-hist-fix-kinetics-simvclinleak-scheme3-part1.py to generate Figure 7 and Table S4.

Figure 8: Run plot-fitted-parameters-fix-kinetics-simvclinleak-scheme3.py to generate Figure 8.

Figure S7: Run plot-rmsd-hist-fix-kinetics-simvclinleak-scheme3-part2.py to generate Figure S7.

Figure S8: Run plot-ss-tau.py to generate Figure S8.

Figure S9: Run plot-staircase-difference.py to generate Figure S9.

Table S3: Run print-tex-table.py to generate Table S3.

Extra results mentioned but not shown in the paper

Results for fitting the full voltage-clamp model to data: Run fit-full2vclinleak.sh.

Results for 'Hypothesis 3':

All results are cached, so all figures can be re-generated by simply running the figure plots. All results for 'Hypothesis 3' can be reproduced by running:

1. Run fit-simvclinleak.sh to reproduce 'Hypothesis 3' results.
2. Run compute-rmsd-hist-fit-simvclinleak.py to recompute all the RRMSE values for 'Hypothesis 3'.

To re-generate figures:

• An equivalent of Figure 7 for 'Hypothesis 3': Run plot-rmsd-hist-independent-v-scheme3-v-simlinleak-part1.py.
• An equivalent of Figure 8 for 'Hypothesis 3': Run plot-param-fit-simvclinleak-artefacts.py.