Panama: An Open-Source Educational App for Ion Channel Biophysics Simulation.

Binita Rajbanshi,Anuj Guruacharya

doi:10.3389/fninf.2022.813940

Binita Rajbanshi, Anuj Guruacharya

Open Access

https://doi.org/10.3389/fninf.2022.813940

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Abstract

This article describes an open-source educational software, called Panama, developed using R, that simulates the biophysics of voltage-gated ion channels. It is made publicly available as an R package called Panama and as a web app at http://www.neuronsimulator.com. A need for such a tool was observed after surveying available software packages. Available packages are either not robust enough to simulate multiple ion channels, too complicated, usable only as desktop software, not optimized for mobile devices, not interactive, lack intuitive graphical controls, or not appropriate for educational purposes. This app simulates the physiology of voltage-gated sodium, potassium, and chlorine channels; A channel; M channel; AHP channel; calcium-activated potassium channel; transient-calcium channel; and leak-calcium channel, under current-clamp or voltage-clamp conditions. As the input values on the app are changed, the output can be instantaneously visualized on the web browser and downloaded as a data table to be further analyzed in a spreadsheet program. This app is a first-of-its-kind, mobile-friendly, and touchscreen-friendly online tool that can be used as an installable R package. It has intuitive touch-optimized controls, instantaneous graphical output, and yet is pedagogically robust for educational purposes.

Highlights

The Hodgkin–Huxley (Hodgkin et al, 1952) model is one of the fundamental neuronal models
The 11 channels simulated in this app were voltage-gated sodium, potassium, and chloride channels; calcium-activated potassium channels (KCa); T-type calcium channels (CaT); L-type calcium channels (CaL), leak sodium (NaLeak), and leak potassium (KLeak) channels; A current channels; M current channels; and
Each channel was represented by its maximal conductance or permeability, its ionic current (In), its reversal potential (En), and its associated gating parameters

Summary

INTRODUCTION

The Hodgkin–Huxley (Hodgkin et al, 1952) model is one of the fundamental neuronal models. Its mathematical form is a set of differential equations that are used before moving on to more complex models Computational simulations using this model strengthen the concepts of action potentials and ion channels. Existing simulation programs, such as NEURON (Hines and Carnevale, 1997) and GENESIS (Bower et al, 2003), serve as powerful tools for simulating the response of whole-cell or singlechannel parameters to electrical or pharmacological stimuli. A new web app for simulating the biophysics of voltage-gated ion channels is described It has been made publicly available at http://www.neuronsimulator.com and as a downloadable R package called Panama through GitHub. Its associated scripts are available at https://github. Current, and conductance values as graphs for each ion channel

METHODS

RESULTS AND DISCUSSION

DATA AVAILABILITY STATEMENT