An Individual-based Probabilistic Model for Fish Stock Simulation

We define an individual-based probabilistic model of a sole (Solea solea) behaviour. The individual model is given in terms of an Extended Probabilistic Discrete Timed Automaton (EPDTA), a new formalism that is introduced in the paper and that is shown to be interpretable as a Markov decision process. A given EPDTA model can be probabilistically model-checked by giving a suitable translation into syntax accepted by existing model-checkers. In order to simulate the dynamics of a given population of soles in different environmental scenarios, an agent-based simulation environment is defined in which each agent implements the behaviour of the given EPDTA model. By varying the probabilities and the characteristic functions embedded in the EPDTA model it is possible to represent different scenarios and to tune the model itself by comparing the results of the simulations with real data about the sole stock in the North Adriatic sea, available from the recent project SoleMon. The simulator is presented and made available for its adaptation to other species.Comment: In Proceedings AMCA-POP 2010, arXiv:1008.314

Agent-Based Models and Simulations in Economics and Social Sciences: from conceptual exploration to distinct ways of experimenting

Now that complex Agent-Based Models and computer simulations spread over economics and social sciences - as in most sciences of complex systems -, epistemological puzzles (re)emerge. We introduce new epistemological tools so as to show to what precise extent each author is right when he focuses on some empirical, instrumental or conceptual significance of his model or simulation. By distinguishing between models and simulations, between types of models, between types of computer simulations and between types of empiricity, section 2 gives conceptual tools to explain the rationale of the diverse epistemological positions presented in section 1. Finally, we claim that a careful attention to the real multiplicity of denotational powers of symbols at stake and then to the implicit routes of references operated by models and computer simulations is necessary to determine, in each case, the proper epistemic status and credibility of a given model and/or simulation

A modelling approach towards Epidermal homoeostasis control

In order to grasp the features arising from cellular discreteness and individuality, in large parts of cell tissue modelling agent-based models are favoured. The subclass of off-lattice models allows for a physical motivation of the intercellular interaction rules. We apply an improved version of a previously introduced off-lattice agent-based model to the steady-state flow equilibrium of skin. The dynamics of cells is determined by conservative and drag forces,supplemented with delta-correlated random forces. Cellular adjacency is detected by a weighted Delaunay triangulation. The cell cycle time of keratinocytes is controlled by a diffusible substance provided by the dermis. Its concentration is calculated from a diffusion equation with time-dependent boundary conditions and varying diffusion coefficients. The dynamics of a nutrient is also taken into account by a reaction-diffusion equation. It turns out that the analysed control mechanism suffices to explain several characteristics of epidermal homoeostasis formation. In addition, we examine the question of how {\em in silico} melanoma with decreased basal adhesion manage to persist within the steady-state flow-equilibrium of the skin.Interestingly, even for melanocyte cell cycle times being substantially shorter than for keratinocytes, tiny stochastic effects can lead to completely different outcomes. The results demonstrate that the understanding of initial states of tumour growth can profit significantly from the application of off-lattice agent-based models in computer simulations.Comment: 23 pages, 7 figures, 1 table; version that is to appear in Journal of Theoretical Biolog

Multi-level agent-based modeling - A literature survey

During last decade, multi-level agent-based modeling has received significant and dramatically increasing interest. In this article we present a comprehensive and structured review of literature on the subject. We present the main theoretical contributions and application domains of this concept, with an emphasis on social, flow, biological and biomedical models.Comment: v2. Ref 102 added. v3-4 Many refs and text added v5-6 bibliographic statistics updated. v7 Change of the name of the paper to reflect what it became, many refs and text added, bibliographic statistics update

Agent-Based Models and Simulations in Economics and Social Sciences

Now that complex Agent-Based Models and computer simulations spread over economics and social sciences - as in most sciences of complex systems -, epistemological puzzles (re)emerge. We introduce new epistemological concepts so as to show to what extent authors are right when they focus on some empirical, instrumental or conceptual significance of their model or simulation. By distinguishing between models and simulations, between types of models, between types of computer simulations and between types of empiricity obtained through a simulation, section 2 gives the possibility to understand more precisely - and then to justify - the diversity of the epistemological positions presented in section 1. Our final claim is that careful attention to the multiplicity of the denotational powers of symbols at stake in complex models and computer simulations is necessary to determine, in each case, their proper epistemic status and credibility.Agent-Based Models and Simulations ; Epistemology ; Economics ; Social Sciences ; Conceptual Exploration ; Model World ; Credible World ; Experiment ; Denotational Hierarchy

TRAINING HIGHER EDUCATION BIOSCIENCE STUDENTS WITH VIRTUAL REALITY SIMULATOR

Laboratory training is the cornerstone of science education in higher education. However, in several cases hands-on experimental procedures are not possible, and therefore technology provide alternative educational methods. One of the rapidly evolving technologies, namely Virtual Reality (VR) can offer multiple benefits in laboratory training through the development of simulations and virtual laboratories that support, facilitate, and promote an effective their learning experience. We present an empirical research carried out at the Department of Molecular Biology and Genetics of the Democritus University of Thrace during the winter semester of the academic year 2020-2021. 51 undergraduate students carried out a Virtual Reality activity aiming to train them to the use of a Class II Biosafety Cabinet (BSC) in an immersive virtual environment. Our results show that VR approach was highly and enthusiastically accepted by the students; they reported that they had an authentic learning experience which enabled them to better achieve the learning objectives. However, in some cases symptoms like dizziness and blurry image were reported most likely due to equipment, showing that improvement of the equipment used in VR is needed. Article visualizations

Basis Token Consistency: A Practical Mechanism for Strong Web Cache Consistency

With web caching and cache-related services like CDNs and edge services playing an increasingly significant role in the modern internet, the problem of the weak consistency and coherence provisions in current web protocols is becoming increasingly significant and drawing the attention of the standards community [LCD01]. Toward this end, we present definitions of consistency and coherence for web-like environments, that is, distributed client-server information systems where the semantics of interactions with resource are more general than the read/write operations found in memory hierarchies and distributed file systems. We then present a brief review of proposed mechanisms which strengthen the consistency of caches in the web, focusing upon their conceptual contributions and their weaknesses in real-world practice. These insights motivate a new mechanism, which we call "Basis Token Consistency" or BTC; when implemented at the server, this mechanism allows any client (independent of the presence and conformity of any intermediaries) to maintain a self-consistent view of the server's state. This is accomplished by annotating responses with additional per-resource application information which allows client caches to recognize the obsolescence of currently cached entities and identify responses from other caches which are already stale in light of what has already been seen. The mechanism requires no deviation from the existing client-server communication model, and does not require servers to maintain any additional per-client state. We discuss how our mechanism could be integrated into a fragment-assembling Content Management System (CMS), and present a simulation-driven performance comparison between the BTC algorithm and the use of the Time-To-Live (TTL) heuristic.National Science Foundation (ANI-9986397, ANI-0095988

Virtual Reality Games for Motor Rehabilitation

This paper presents a fuzzy logic based method to track user satisfaction without the need for devices to monitor users physiological conditions. User satisfaction is the key to any product’s acceptance; computer applications and video games provide a unique opportunity to provide a tailored environment for each user to better suit their needs. We have implemented a non-adaptive fuzzy logic model of emotion, based on the emotional component of the Fuzzy Logic Adaptive Model of Emotion (FLAME) proposed by El-Nasr, to estimate player emotion in UnrealTournament 2004. In this paper we describe the implementation of this system and present the results of one of several play tests. Our research contradicts the current literature that suggests physiological measurements are needed. We show that it is possible to use a software only method to estimate user emotion

Overview on agent-based social modelling and the use of formal languages

Transdisciplinary Models and Applications investigates a variety of programming languages used in validating and verifying models in order to assist in their eventual implementation. This book will explore different methods of evaluating and formalizing simulation models, enabling computer and industrial engineers, mathematicians, and students working with computer simulations to thoroughly understand the progression from simulation to product, improving the overall effectiveness of modeling systems.Postprint (author's final draft