AUTHOR=Rajbanshi Binita , Guruacharya Anuj 

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

JOURNAL=Frontiers in Neuroinformatics

VOLUME=Volume 16 - 2022

YEAR=2022

URL=https://www.frontiersin.org/journals/neuroinformatics/articles/10.3389/fninf.2022.813940

DOI=10.3389/fninf.2022.813940

ISSN=1662-5196

ABSTRACT=This paper 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 a 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 touch screen 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.