Formalizing knowledge in multi-scale agent-based simulations

Abstract

Multi-scale, agent-based simulations of cellular and tissue biology are increasingly common. These simulations combine and integrate a range of components from different domains. Simulations continuously create, destroy and reorganize constituent elements causing their interactions to dynamically change. For example, the multi-cellular tissue development process coordinates molecular, cellular and tissue scale objects with biochemical, biomechanical, spatial and behavioral processes to form a dynamic network. Different domain specific languages can describe these components in isolation, but cannot describe their interactions. No current programming language is designed to represent in human readable and reusable form the domain specific knowledge contained in these components and interactions. We present a new hybrid programming language paradigm that naturally expresses the complex multi-scale objects and dynamic interactions in a unified way and allows domain knowledge to be captured, searched, formalized, extracted and reused.

Simulation Modeling in Supply Chain Management Research of Ethanol: A Review

“…Similar to DES, it enables us to describe the operations of a system in detail. However, it considers continuous-event instead of discrete-event [47]. This implies that ABS could mimic the characteristics of a system more accurately than DES in a continuous environment even though it requires a higher computational demand [48,49].…”

Real-Time Interactive Modeling and Simulation in Biological Physics and Active Matter with Mechanica

“…The first and foremost requirement of any simulation software is the ability to actually represent, model, simulate and analyze things in the problem domain. In previous papers, we have made a series of studies in what are the core mechanisms in active matter and biological physics [29,28,26,25,24]. We have identified the core physical concepts or mechanisms that we believe can serve as a basis set of fundamental building blocks with which to construct biological and active matter simulations.…”