A mathematical framework for agent based models of complex biological networks

DOI10.1007/S11538-010-9582-8zbMATH Open1225.92001arXiv1006.0408OpenAlexW3105105868WikidataQ44959902 ScholiaQ44959902MaRDI QIDQ644577FDOQ644577

Authors: Franziska Hinkelmann, David Murrugarra, Abdul Salam Jarrah, Reinhard Laubenbacher 

Publication date: 4 November 2011

Published in: Bulletin of Mathematical Biology (Search for Journal in Brave)

Abstract: Agent-based modeling and simulation is a useful method to study biological phenomena in a wide range of fields, from molecular biology to ecology. Since there is currently no agreed-upon standard way to specify such models it is not always easy to use published models. Also, since model descriptions are not usually given in mathematical terms, it is difficult to bring mathematical analysis tools to bear, so that models are typically studied through simulation. In order to address this issue, Grimm et al. proposed a protocol for model specification, the so-called ODD protocol, which provides a standard way to describe models. This paper proposes an addition to the ODD protocol which allows the description of an agent-based model as a dynamical system, which provides access to computational and theoretical tools for its analysis. The mathematical framework is that of algebraic models, that is, time-discrete dynamical systems with algebraic structure. It is shown by way of several examples how this mathematical specification can help with model analysis.

Full work available at URL: https://arxiv.org/abs/1006.0408

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zbMATH Keywords

algebraic models

Mathematics Subject Classification ID

Dynamical systems in biology (37N25) Probabilistic models, generic numerical methods in probability and statistics (65C20) General biology and biomathematics (92B05)

Cites Work

• SINGULAR
• The dynamics of conjunctive and disjunctive Boolean network models
• Title not available (Why is that?)

Cited In (17)

• Controlled stochastic partial differential equations for rabbits on a grassland
• Control of intracellular molecular networks using algebraic methods
• Title not available (Why is that?)
• Mathematical Analysis of a PDE System for Biological Network Formation
• Dynamics of semilattice networks with strongly connected dependency graph
• Pinning synchronization of fractional order complex-variable dynamical networks with time-varying coupling
• Optimal harvesting for a predator-prey agent-based model using difference equations
• From Boolean networks to linear dynamical systems: a simplified route
• Computational methods for asynchronous basins
• Computational framework to capture the spatiotemporal density of cells with a cumulative environmental coupling
• Conditional tests on basins of attraction with finite fields
• The number of multistate nested canalyzing functions
• Boolean network analysis through the joint use of linear algebra and algebraic geometry
• Vanishing configurations in network dynamics with asynchronous updates
• Transactions on Computational Systems Biology III
• Global Density Analysis for an Off-Lattice Agent-Based Model
• Towards a Bayesian Analysis of Migration Pathways Using Chain Event Graphs of Agent Based Models

Uses Software

• Macaulay2
• SINGULAR

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