BioModME for building and simulating dynamic computational models of complex biological systems

Justin A Womack; Viren Shah; Said H Audi; Scott S Terhune; Ranjan K Dash

doi:10.1093/bioadv/vbae023

BioModME for building and simulating dynamic computational models of complex biological systems

Bioinform Adv. 2024 Feb 20;4(1):vbae023. doi: 10.1093/bioadv/vbae023. eCollection 2024.

Authors

Justin A Womack^{1

2}, Viren Shah^{1

2}, Said H Audi^{1

2}, Scott S Terhune^{1

3}, Ranjan K Dash^{1

2

4}

Affiliations

¹ Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, United States.
² Department of Biomedical Engineering, Marquette University, Milwaukee, WI 53223, United States.
³ Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226, United States.
⁴ Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, United States.

Abstract

Summary: Molecular mechanisms of biological functions and disease processes are exceptionally complex, and our ability to interrogate and understand relationships is becoming increasingly dependent on the use of computational modeling. We have developed "BioModME," a standalone R-based web application package, providing an intuitive and comprehensive graphical user interface to help investigators build, solve, visualize, and analyze computational models of complex biological systems. Some important features of the application package include multi-region system modeling, custom reaction rate laws and equations, unit conversion, model parameter estimation utilizing experimental data, and import and export of model information in the Systems Biology Matkup Language format. The users can also export models to MATLAB, R, and Python languages and the equations to LaTeX and Mathematical Markup Language formats. Other important features include an online model development platform, multi-modality visualization tool, and efficient numerical solvers for differential-algebraic equations and optimization.

Availability and implementation: All relevant software information including documentation and tutorials can be found at https://mcw.marquette.edu/biomedical-engineering/computational-systems-biology-lab/biomodme.php. Deployed software can be accessed at https://biomodme.ctsi.mcw.edu/. Source code is freely available for download at https://github.com/MCWComputationalBiologyLab/BioModME.