Skip to content

Latest commit

 

History

History

model-cell-experiments

Folders and files

NameName
Last commit message
Last commit date

parent directory

..
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Application to electrical model cells

All electrical model cell experiments are within this directory.

Figure 4: Run simulate-all.py with argument staircase.

Figure 5A, B: Run predict-mc3-all.sh.

Table 2, S1: Run fit-mc.py and fit-mc3.py to obtain the fitting results. Run print-tex-table.py to generate the table.

Figure S4A, B, C, d: Run simulate-all.sh.

Figure S5A, B: Run predict-mc.py with argument staircase (A) and ap-lei (B).

Table S2: To generate results for Table S2, run fit-mc3simvc.py.

Forward simulations

simulate-mcnocomp.py: Forward simulate Type I Model Cell no compensations experiment. simulate-mc3nocomp.py: Forward simulate Type II Model Cell no compensations experiment. simulate-mcauto.py: Forward simulate Type I Model Cell HEKA automatic estimated compensations experiment. simulate-mc3auto.py: Forward simulate Type II Model Cell HEKA automatic estimated compensations experiment.

All of them run with argument [str:which_sim]: staircase, sinewave, ap-lei.

Parameter inference

fit-mc.py: Parameter inference for Type I Model Cell no compensations experiment. fit-mc3.py: Parameter inference for Type II Model Cell no compensations experiment. fit-mc3simvc.py: Parameter inference for Type II Model Cell no compensations experiment with simplified voltage-clamp experiment model.

Predictions using inferred parameters

predict-mc.py: Predictions from fitted model using fit-mc.py. predict-mc3.py: Predictions from fitted model using fit-mc3.py. predict-mc3simvc.py: Predictions from fitted model using fit-mc3simvc.py.

All of them run with argument [str:which_predict]: staircase, sinewave, ap-lei.

Directories

data: Contains raw bundle dat data from HEKA PatchMaster. out: Contains fitting results and parameters. figs: Contains all output figures.