Agent-Based Modelling in Cellular Biology - Are we flexible yet?

TL;DR

This paper critiques current cellular agent-based modeling tools, highlighting their lack of flexibility in representing biological complexity, which impedes progress in the field.

Contribution

It provides an analysis of existing ABM frameworks across domains and identifies their limitations in flexibility for biological modeling.

Findings

Existing ABMs lack sufficient flexibility.

Limited adaptability hampers biological complexity representation.

Flexibility improvements could advance cellular biology modeling.

Abstract

Cellular Agent-Based Models are commonly employed to describe a variety biological systems. Over the course of the past years, many modeling tools have emerged which solve particular research questions. In this short opinion piece, we argue that existing frameworks lack flexibility compared to the inherent underlying complexity that they should be able to represent. We extract overarching principles of widely used software solutions across multiple domains and compare these with existing Agent-Based Models (ABMs). We come to the conclusion that existing ABMs lack in flexibility which hinders overall progress of the field.