Trajectory Matching-Random Walk Feasibility Sampling Algorithm
Overview
TM-RWFS is a computational algorithm for simulating heterogeneous dynamics in mechanistic mathematical models.
The repository provides data corresponding to all the models investigated in the study. The Lotka-Volterra model is used as an example to demonstrate the implementation of the TM-RWFS algorithm.
Requirements
• Julia ≥ 1.10
• Installation guide: https://julialang.org/install/
Inputs
• Experimental or clinical data
• Mathematical model (ODEs, DDEs), parameters best fit values
• TM-RWFS parameters
Outputs
• Accepted trajectories
• Parameters distributions
• Execution time
Code Availability
This repository contains code that reproduces the results for the Lotka–Volterra model as an example of the TM-RWFS algorithm's implementation.
The archived version of the repository is available on Zenodo:
https://doi.org/10.5281/zenodo.23768581
Data Sources
Data corresponding to all models investigated in the study are provided in this repository.
Experimental data were extracted from figures in previously published studies.
The original data sources are:
Case Study 1: Toni, T., Welch, D., Strelkowa, N., Ipsen, A. and Stumpf, M. P. (2009). Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems. J. R. Soc. Interface. 6, 187-202. https://doi.org/10.1098/rsif.2008.0172.
Case Study 2A: Smith, A. P., Moquin, D. J., Bernhauerova, V. and Smith, A. M. (2018). Influenza virus infection model with density dependence supports biphasic viral decay. Front. Microbiol. 9, 1554. https://doi.org/10.3389/fmicb.2018.01554.
Case Study 2B: Myers, M. A., Smith, A. P., Lane, L. C., Moquin, D. J., Aogo, R., Woolard, S., Thomas, P., Vogel, P. , Smith, A. M. (2021). Dynamically linking influenza virus infection kinetics, lung injury, inflammation, and disease severity. Elife 10, e68864. https://doi.org/10.7554/elife.68864.
Case Study 3: Wares, J. R., Crivelli, J. J., Yun, C.-O., Choi, I.-K., Gevertz, J. L. and Kim, P. S. (2015). Treatment strategies for combining immunostimulatory oncolytic virus therapeutics with dendritic cell injections. Math. Biosci. Eng. 12, 1237-1256. https://doi.org/10.3934/mbe.2015.12.1237.
Citation
• https://www.biorxiv.org/content/10.1101/2025.09.26.678800v2
Supplementary questions
For any questions regarding the code, please write to fatemeh.beigmohammadi@umontreal.ca