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Rules of Engagement: A Guide to Developing Agent-Based Models.

Marc Griesemer1, Suzanne S Sindi2

  • 1Controls and Data Systems Division, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.

Methods in Molecular Biology (Clifton, N.J.)
|October 31, 2021
PubMed
Summary
This summary is machine-generated.

Agent-based models (ABMs) simulate populations of interacting individuals. This guide details developing ABMs, using a microbial community case study on cellular dynamics influenced by individual processes and cell-cell contact.

Keywords:
Agent-based modelsIndividual-based modelsLattice-freeStochastic simulations

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Area of Science:

  • Computational Biology
  • Ecology
  • Systems Biology

Background:

  • Agent-based models (ABMs) simulate autonomous individuals and their interactions.
  • ABMs are versatile, applied across engineering, economics, ecology, and biology.
  • Developing ABMs requires understanding conceptual issues, implementation, and potential pitfalls.

Purpose of the Study:

  • To guide users in developing agent-based models from first principles.
  • To present a case study of an ABM for microbial community cellular dynamics.
  • To illustrate how individual cell processes and interactions influence multi-scale dynamics.

Main Methods:

  • Development of a lattice-free agent-based model for individual cells.
  • Modeling cell actions: growth, movement, and division.
  • Incorporating influences of cell cycle and cell-cell contact (adhesion, contact inhibition).

Main Results:

  • The developed ABM captures multi-scale dynamics of cellular interactions.
  • Individual cell processes and inter-cellular contacts were successfully modeled.
  • The model provides insights into microbial community behavior.

Conclusions:

  • Agent-based modeling offers a powerful framework for studying complex biological systems.
  • This approach effectively simulates cellular interactions and community dynamics.
  • Understanding individual behavior and interactions is key to predicting population-level outcomes.