Doctoral Thesis Defense: Spatial Interactive Agent-based Models at Multiple Levels of Biological Organization

December 11, 2018
11:00 AM
Halligan 111B
Speaker: Giordano Ferreira
Host: Matthias Scheutz

Abstract

Most biological systems are hard to investigate in the laboratory or in the field. Computational modeling has been used to help researchers to generate novel hypotheses to be tested empirically. Agent-based modeling (ABM) has emerged as a viable modeling paradigm in biology. ABM is a bottom-up approach in which the phenomena of interest emerge from behavioral rules of the minimal component of the model: the agent. ABMs for biology exist at different scales, from the molecular scale in which agents are molecules inside a cell to the macroscopic scale in which agents are animals in some social context. In addition, some ABMs are spatially explicit and some models allow agents to interact with each other. This dissertation focuses on Interactive Spatial Agent-based Models for biology at different scales. It describes the Interactive Spatial Agent-based Model Framework (IS-ABM Framework), a standard way to plan agent-based models for biological systems. The goal of the IS-ABM Framework is to help newcomers to the ABM community with the modeling procedure. This dissertation also presents two Interactive Spatial Agent-based Models for two distinct biological systems. At the macroscopic scale, the focus is to understand social behaviors of animals. Specifically, territory exploration tasks in which individuals must visit checkpoints distributed across an environment. Checkpoints have a quality that can be sensed by individuals. Individuals must balance the quality of the checkpoints with the costs to reach them. The main instance explored here is the mating selection task. At the microscopic scale, this dissertation presents a proof-of-concept model to explore the regeneration process in Planaria. This model investigates how morphological information can be stored and edited without genetic modifications after the full development of the organism. Using only local communication, this mechanism replicates various regeneration capabilities displayed by Planaria such as random cell death, tissue removal, reliability against noise, stem cell migration and proliferation.