High-Performance Agent-Based Modeling Applied to Vocal Fold Inflammation and Repair

Authored by Nuttiiya Seekhao, Caroline Shung, Joseph JaJa, Luc Mongeau, Nicole Y K Li-Jessen

Date Published: 2018

DOI: 10.3389/fphys.2018.00304

Sponsors: United States National Institutes of Health (NIH) United States National Science Foundation (NSF)

Platforms: C++

Model Documentation: Other Narrative Flow charts Pseudocode Mathematical description

Model Code URLs: https://github.com/VF-ABM/hpc-abm-vf-version_0_6

Abstract

Fast and accurate computational biology models offer the prospect of accelerating the development of personalized medicine. A tool capable of estimating treatment success can help prevent unnecessary and costly treatments and potential harmful side effects. A novel high-performance Agent-Based Model (ABM) was adopted to simulate and visualize multi-scale complex biological processes arising in vocal fold inflammation and repair. The computational scheme was designed to organize the 3D ABM sub-tasks to fully utilize the resources available on current heterogeneous platforms consisting of multi-core CPUs and many-core GPUs. Subtasks are further parallelized and convolution-based diffusion is used to enhance the performance of the ABM simulation. The scheme was implemented using a client-server protocol allowing the results of each iteration to be analyzed and visualized on the server (i.e., in-situ) while the simulation is running on the same server. The resulting simulation and visualization software enables users to interact with and steer the course of the simulation in real-time as needed. This high-resolution 3D ABM framework was used for a case study of surgical vocal fold injury and repair. The new framework is capable of completing the simulation, visualization and remote result delivery in under 7 s per iteration, where each iteration of the simulation represents 30 min in the real world. The case study model was simulated at the physiological scale of a human vocal fold. This simulation tracks 17 million biological cells as well as a total of 1.7 billion signaling chemical and structural protein data points. The visualization component processes and renders all simulated biological cells and 154 million signaling chemical data points. The proposed high-performance 3D ABM was verified through comparisons with empirical vocal fold data. Representative trends of biomarker predictions in surgically injured vocal folds were observed.

Tags

Simulation Agent-based modeling inflammation wound healing systems biology high-performance computing Multiscale vocal fold Acute phonotrauma Rat Science Work Fibroblasts Disorders Biosimulation In situ visualization Group box 1 Voice problems Hyaluronan