Table 7.

List of software for agent-based and multi-scale modeling.

Software (implementation)	Application	References
BacArena (R)	Agent-based modeling utilizing constraint-based metabolic modeling	Bauer et al., 2017
COMETS (desktop application/ Python/ MATLAB/ command line)	Agent-based modeling utilizing constraint-based metabolic modeling	Dukovski et al., 2021
IndiMESH (MATLAB)	Agent-based modeling specialized to soil ecosystems	Borer et al., 2019
Morpheus (desktop application)	Modeling and simulation of multi-cellular and multi-scale systems	Starruß et al., 2014