Add Hypothesis 3 results

Author: chonlei

README.md

@@ -30,6 +30,7 @@ It contains results and code to reproduce Figure S6.
 [fit-same-kinetics](./fit-same-kinetics): Application of the voltage-clamp experiment model to data in [hERGRapidCharacterisation](https://github.com/CardiacModelling/hERGRapidCharacterisation).
 
 It contains results and code to reproduce Figures 7, 8; Figures S7, S8, S9; Tables S3, S4.
+It also contains results and code that are mentioned but not shown in the paper: full voltage-clamp experiment model fitting to hERG data; independent kinetics with independent artefacts 'Hypothesis 3'.
 
 ### Supporting files
 

fit-same-kinetics/README.md

@@ -1,11 +1,11 @@
 # Application to real hERG data
 
 All results are cached, so all figures can be re-generated by simply running the figure plots.
-All results can be reproduced by running:
+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.
+2. Run `fit-simvclinleak-scheme3-parallel.py` to run [fits](out/herg25oc1-scheme3-simvclinleak) with Eq. (4.14) using Algorithm S1.
+3. Run `compute-rmsd-hist-fix-kinetics-simvclinleak-scheme3.py` to compute all the [RRMSE values](out/rmsd-hist-herg25oc1-fixkinetics-simvclinleak-scheme3).
 
 [Figure 7](figs/rmsd-hist-fix-kinetics-simvclinleak-scheme3-part1.pdf), Table S4: Run `plot-rmsd-hist-fix-kinetics-simvclinleak-scheme3-part1.py` to generate Figure 7 and Table S4.
 
@@ -22,4 +22,8 @@ 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](out/herg25oc1-full2vclinleak): Run `fit-full2vclinleak.sh`.
 
-Results for ['Hypothesis 3'](.): TODO.
+Results for ['Hypothesis 3'](out/herg25oc1-simvclinleak):
+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'](out/rmsd-hist-herg25oc1-fit-simvclinleak).
+3. Run `plot-rmsd-hist-independent-v-scheme3-v-simlinleak-part1.py` to generate [an equivalent of Figure 7 for 'Hypothesis 3'](figs/rmsd-hist-independent-v-scheme3-v-simlinleak-part1.png).
+4. Run  `plot-param-fit-simvclinleak-artefacts.py` to generate [an equivalent of Figure 8 for 'Hypothesis 3'](figs/herg25oc1-simvclinleak-artefacts.png).