HH-Modelica

This repository contains a modular implementation of the Hodgkin-Huxley equations that has two aims:

1. Increase the understandability of the Hodgkin-Huxley model for novices by keeping the amount of variables and equations per component very low and bridging the gap between biological meaning and electrical analogy.
2. Serve as a unifying basis for extensions by experts and therefore facilitate the creation of more complex Hogdkin-Huxley-type models.

Documentation

A HTML documentation of the model can be found on GitHub pages.

Quick guide

To simulate the models in this repository you can use the following steps:

• Download and install OpenModelica.
• Clone this repository with Git or download a ZIP file of the current master branch and extract it with an archive manager of your choice.
• Start the OpenModelica Connection Editor (OMEdit) and open the folder HHmodelica with "File" → "Load Library".
• Open the model you want to simulate, e.g. HHModelica.CompleteModels.HHmodular (select from "Libraries Browser" on the left hand side with a double click).
• Simulate the model with "Simulation" → "Simulate".
• In the "Variables Browser" on the right hand side select the variable clamp.v.

Project structure

• HHmodelica/CompleteModels contains complete Hodgkin-Huxley models that are ready for simulation
  • HHelectric.mo is a model that consists of electric components from the Modelica standard library. It should be mainly used as a reference for how the diagram view of a completely electrical implementation would look. Direct simulation will not yield any usable results as the voltage-dependent change of conductance in ion channels is not included.
  • HHmodular.mo is the main modular implementation. It directly contains all ion channels, the lipid bilayer and the current clamp on one hierarchical layer.
  • HHmodHier.mo is the same as HHmodFlat.mo, but with an additional hierarchical layer that combines lipid bilayer and ion channels to a "membrane" model which is then connected to the current clamp.
  • HHmodular1p.mo is analog to HHmodular.mo, but features a reduced interface that abandons the analogy of an electric circuit by only using a single pin to connect the components. This development branch is discontinued, because I do not think the reduction in the number of equations justifies to break the circuit analogy and therefore make the diagram view less intuitive.
  • HHmono.mo is a "classical" monolithic implementation of the Hogdkin-Huxley equations.
• HHmodelica/Components/package.mo contains components used for the modular models with regular two-pin components.
• HHmodelica/Components/OnePin/package.mo contains components used for the one-pin model HHmodular1p.mo.
• HHmodelica/Components/Icons contains empty models with graphical annotations that are used to give a graphical representation to modular model components.
• img contains SVG images that were used to create the graphical annotations for the component icons (with a currently unpublished Inkscape plugin).
• regRefData is a submodule that links to the repository HH-modelica-ref which contains reference data for the regression tests (see below).
• scripts contains scripts for testing and plotting (see below).

Testing

The file scripts/unittests.jl contains a Julia script that uses OMJulia to interface with the OpenModelica compiler. To install all necessary dependencies you have do the following:

1. Download and install Julia.
2. Run the following commands in a terminal from the repository folder:
   • julia -e 'ENV["PYTHON"]=""; using Pkg; Pkg.add(PackageSpec(url="https://github.com/THM-MoTE/ModelicaScriptingTools.jl.git"))'
   • julia scripts/unittests.jl

Test output

The test suite produces simulation outputs in the folder out (will be created). These outputs are used by the plotting script (see below).

Regression tests

The test suite also contains regression tests that are used to check whether a change in the code has introduced any unforeseen change in the simulation output. For this I store the latest verified simulation results in a separate repository. This is done to ensure that the large (currently ~2MB) data files do not inflate the size of the git history of this project. The reference files are downloaded automatically when you call git submodule update --init.

Plots

The plot from the publication (see below) can be reproduced by calling python plot_compare.py in the scripts directory. The plotting script depends on the data generated by the unit tests (see above) and will generate plots in the folder plots (will be created).

Publication

This project has been published in Frontiers in Physiology - Computational Physiology and Medicine:

C. Schölzel, V. Blesius, G. Ernst, and A. Dominik, “An understandable, extensible, and reusable implementation of the Hodgkin-Huxley equations using Modelica,” Front. Physiol., vol. 11, p. 583203, 2020, doi: 10.3389/fphys.2020.583203.