AUTHOR=Schmid Kerstin , Knote Andreas , Mück Alexander , Pfeiffer Keram , von Mammen Sebastian , Fischer Sabine C. 

TITLE=Interactive, Visual Simulation of a Spatio-Temporal Model of Gas Exchange in the Human Alveolus

JOURNAL=Frontiers in Bioinformatics

VOLUME=Volume 1 - 2021

YEAR=2022

URL=https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2021.774300

DOI=10.3389/fbinf.2021.774300

ISSN=2673-7647

ABSTRACT=In interdisciplinary fields such as systems biology, \blue{\sout{close collaboration} good communication} between experimentalists and theorists is crucial for the success of a project. Theoretical modeling in physiology usually describes complex systems with many interdependencies. On one hand, these models have to be grounded on experimental data. On the other hand, experimenters must be able to \blue{\sout{penetrate the model in its dependencies in order to correctly} understand the interdependent complexities of the theoretical model in order to} interpret the \blue{model's} results in the physiological context. \blue{\sout{When theorists and experimenters collaborate, communicating results and ideas is sometimes challenging.}}
We promote interactive, visual simulations as an engaging way \blue{to present} theoretical models in physiology and to \blue{\sout{thereby advance our understanding of the process of interest.} make complex processes tangible.} \blue{Based on a requirements analysis, we developed a new model for gas exchange in the human alveolus in combination with an interactive simulation software named \textit{Alvin}. \textit{Alvin} exceeds the current standard with its spatio-temporal resolution and a combination of visual and quantitative feedback.} In \textit{Alvin}, the course of the simulation can be traced in a three-dimensional rendering of an alveolus and dynamic plots. The user can interact by configuring essential model parameters. \textit{Alvin} allows to run and compare multiple simulation instances simultaneously. \blue{\sout{The mathematical model was developed with the aim of visualization and the simulation software was engineered based on a requirements analysis.}} \blue{\sout{We designed and developed the mathematical model and the simulation software in parallel and interdependently based on a requirements analysis.}} \blue{\sout{Our work resulted in an integrative gas exchange model and an interactive application that exceed the current standards.}} We exemplified the use of \textit{Alvin} for research by identifying unknown dependencies in published experimental data. Employing a detailed questionnaire, we showed the benefits of \textit{Alvin} for education. We postulate that interactive, visual simulation of theoretical models, as we have implemented with \textit{Alvin} on respiratory processes in the alveolus, can be of great help for communication between specialists and thereby advancing research.