Vivarium: an interface and engine for integrative multiscale modeling in computational biology

Area of Science:

• Computational Biology
• Systems Biology
• Bioinformatics

Background:

• Integrative multiscale modeling combines diverse datasets and strategies to understand complex biological mechanisms.
• Current model development is labor-intensive, requiring significant effort and collaboration on a case-by-case basis.
• Streamlined software tools are crucial for advancing computational biology and facilitating collaborative modeling efforts.

Purpose of the Study:

• Introduce Vivarium, a novel software tool designed to simplify the creation and execution of integrated multiscale biological models.
• Enable computational biologists to easily define, combine, and execute diverse mechanistic models.
• Facilitate collaboration and streamline the development process for complex biological simulations.

Main Methods:

• Vivarium provides an interface to modularize individual models, allowing them to be combined into large composite models.
• The software supports parallelization across multiple CPUs and utilizes a discrete-event simulation engine.
• Demonstrates utility by integrating agent-based models, ODEs, stochastic reaction systems, constraint-based models, solid-body physics, and spatial diffusion.

Main Results:

• Vivarium successfully integrates multiple heterogeneous modeling frameworks into unified, executable multiscale models.
• The software facilitates the creation of complex composite models by enabling modularization and interconnection of individual components.
• Demonstrates the potential for integrating a wide range of biological scales and model types.

Conclusions:

• Vivarium significantly lowers the barrier to entry for developing complex, integrated multiscale biological models.
• The software promotes collaboration and reusability of modeling components within the computational biology community.
• Vivarium is poised to accelerate research in systems biology by enabling more sophisticated and comprehensive simulations.