Overview of the core model of autophagy. A Schematic describing interaction of the four agent types. Each agent is color-coded; phagophores (PP) in grey, autophagosomes (AP) in red, lysosomes (LYS) in yellow and autolysosomes (AL) in purple. Merging arrows represent fusion events between the two agents to form or expand an autolysosome. Arrows marked with BAF indicate inhibition by Bafilomycin A1. Black arrows represent degradation events. B Overview of the ABM parameter set. Agent parameter colors correspond to the color code used in A. C Schematic of the implemented fitting process to find the best parameter set, performed using a genetic algorithm in combination with a predefined fitness function.