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Experimental measurements from guinea pig ventricular myocytes of dynamic clamp perturbations are used to fit the behavior of the Livshitz Rudy 2009 ventricular model.

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Model fitting using experimental dynamic clamp perturbations

Introduction

Experimental measurements from guinea pig ventricular myocytes of dynamic clamp perturbations are used to fit the behavior of the Livshitz Rudy 2009 ventricular model. Contains experimental data from 14 cells (Cell_1 - Cell_14) as well as the Livshitz Rudy 2009 model itself (Cell_15).

References:

  • Devenyi, Ryan A., et al. "Differential roles of two delayed rectifier potassium currents in regulation of ventricular action potential duration and arrhythmia susceptibility." The Journal of physiology 595.7 (2017): 2301-2317.
  • Livshitz, Leonid, and Yoram Rudy. "Uniqueness and stability of action potential models during rest, pacing, and conduction using problem-solving environment." Biophysical journal 97.5 (2009): 1265-1276.

Protocol files

These files contain the cell membrane capacitance and injected current of the dynamic clamp experiment. The files are organized by row:

  1. Pacing current injection
  2. IKr current injection
  3. IKs current injection
  4. ICaL current injection
  5. IK1 current injection
  6. ICaT current injection
  7. INaK current injection
  8. INCX current injection
  9. Cell membrane capacitance

Objective files

These files contain cell membrane voltage during each dynamic clamp perturbation. The files are organized by row:

  1. Static pacing membrane voltage response
  2. IKr - membrane voltage response
  3. IKs - membrane voltage response
  4. ICaL - membrane voltage response
  5. IK1 - membrane voltage response
  6. ICaT - membrane voltage response
  7. INaK - membrane voltage response
  8. INCX - membrane voltage response

Libraries

A genetic algorithm and the Livshitz Rudy 2009 model used in the dynamic clamp experiments have been added to this repository as subtrees. If you wish to update the libraries, you must first add the remote repository and merge in any new changes.

Analysis and execution scripts

Located in the analysis/ directory.

  • Nominal_Model_Fitting - The genetic algorithm is used to fit the model to objective data created using the nominal parameters of the model. In short, the ideal fit has an error is ~0 with all parameters set to 1.0.
  • Simulation_vs_Objective - A comparison is made between the full dynamic clamp simulation and the simulation run during the GA individual evaluations.

Running the fitting

The fitting executable requires 3 arguments:

  • Objective file
  • Protocol file
  • Genetic algorithm settings file

An example command to fit the model to nominal parameters is as follows:

make && ./GA_Fitting objectives/Objective_GA_Protocol_Simulation.dat protocols/Protocol_DynClamp_Simulation.dat settings.ga

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Experimental measurements from guinea pig ventricular myocytes of dynamic clamp perturbations are used to fit the behavior of the Livshitz Rudy 2009 ventricular model.

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