BioModME for building and simulating dynamic computational models of complex biological systems
Justin A Womack1,2, Viren Shah1,2, Said H Audi1,2
1Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, United States.
Bioinformatics Advances
|March 8, 2024
Summary
BioModME is a new R-based web application that simplifies computational modeling for complex biological systems. It offers tools for building, solving, and analyzing models, aiding research in biology and disease processes.
Area of Science:
- Computational Biology
- Systems Biology
- Bioinformatics
Background:
- Understanding complex molecular mechanisms in biology and disease requires advanced computational modeling.
- Existing tools may lack the necessary features for intuitive model development and analysis.
- There is a growing need for user-friendly platforms to facilitate computational modeling in life sciences.
Purpose of the Study:
- To introduce BioModME, a novel R-based web application package for computational modeling of biological systems.
- To provide an intuitive graphical user interface (GUI) for building, solving, visualizing, and analyzing complex biological models.
- To offer a comprehensive suite of features for advanced computational modeling tasks.
Main Methods:
- Development of a standalone R-based web application package named BioModME.
- Implementation of a comprehensive graphical user interface (GUI) for user interaction.
- Integration of features such as multi-region system modeling, custom reaction rate laws, unit conversion, and parameter estimation.
- Support for import/export in Systems Biology Markup Language (SBML) format.
- Inclusion of model export to MATLAB, R, and Python, and equation export to LaTeX and MathML.
- Provision of an online model development platform and multi-modality visualization tools.
- Integration of efficient numerical solvers for differential-algebraic equations and optimization.
Main Results:
- BioModME provides an intuitive platform for creating, solving, and analyzing computational models of biological systems.
- The application supports advanced features including parameter estimation from experimental data and multi-region modeling.
- Models can be seamlessly exchanged with other platforms and programming languages (SBML, MATLAB, R, Python).
- Users benefit from an online development environment, visualization tools, and robust numerical solvers.
Conclusions:
- BioModME significantly enhances the ability of investigators to model complex biological systems.
- The user-friendly interface and comprehensive features lower the barrier to entry for computational modeling in biological research.
- This tool facilitates a deeper understanding of molecular mechanisms underlying biological functions and disease processes.
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