80,602 research outputs found
Simulation of networks of spiking neurons: A review of tools and strategies
We review different aspects of the simulation of spiking neural networks. We
start by reviewing the different types of simulation strategies and algorithms
that are currently implemented. We next review the precision of those
simulation strategies, in particular in cases where plasticity depends on the
exact timing of the spikes. We overview different simulators and simulation
environments presently available (restricted to those freely available, open
source and documented). For each simulation tool, its advantages and pitfalls
are reviewed, with an aim to allow the reader to identify which simulator is
appropriate for a given task. Finally, we provide a series of benchmark
simulations of different types of networks of spiking neurons, including
Hodgkin-Huxley type, integrate-and-fire models, interacting with current-based
or conductance-based synapses, using clock-driven or event-driven integration
strategies. The same set of models are implemented on the different simulators,
and the codes are made available. The ultimate goal of this review is to
provide a resource to facilitate identifying the appropriate integration
strategy and simulation tool to use for a given modeling problem related to
spiking neural networks.Comment: 49 pages, 24 figures, 1 table; review article, Journal of
Computational Neuroscience, in press (2007
Principles and Concepts of Agent-Based Modelling for Developing Geospatial Simulations
The aim of this paper is to outline fundamental concepts and principles of the Agent-Based Modelling (ABM) paradigm, with particular reference to the development of geospatial simulations. The paper begins with a brief definition of modelling, followed by a classification of model types, and a comment regarding a shift (in certain circumstances) towards modelling systems at the individual-level. In particular, automata approaches (e.g. Cellular Automata, CA, and ABM) have been particularly popular, with ABM moving to the fore. A definition of agents and agent-based models is given; identifying their advantages and disadvantages, especially in relation to geospatial modelling. The potential use of agent-based models is discussed, and how-to instructions for developing an agent-based model are provided. Types of simulation / modelling systems available for ABM are defined, supplemented with criteria to consider before choosing a particular system for a modelling endeavour. Information pertaining to a selection of simulation / modelling systems (Swarm, MASON, Repast, StarLogo, NetLogo, OBEUS, AgentSheets and AnyLogic) is provided, categorised by their licensing policy (open source, shareware / freeware and proprietary systems). The evaluation (i.e. verification, calibration, validation and analysis) of agent-based models and their output is examined, and noteworthy applications are discussed.Geographical Information Systems (GIS) are a particularly useful medium for representing model input and output of a geospatial nature. However, GIS are not well suited to dynamic modelling (e.g. ABM). In particular, problems of representing time and change within GIS are highlighted. Consequently, this paper explores the opportunity of linking (through coupling or integration / embedding) a GIS with a simulation / modelling system purposely built, and therefore better suited to supporting the requirements of ABM. This paper concludes with a synthesis of the discussion that has proceeded. The aim of this paper is to outline fundamental concepts and principles of the Agent-Based Modelling (ABM) paradigm, with particular reference to the development of geospatial simulations. The paper begins with a brief definition of modelling, followed by a classification of model types, and a comment regarding a shift (in certain circumstances) towards modelling systems at the individual-level. In particular, automata approaches (e.g. Cellular Automata, CA, and ABM) have been particularly popular, with ABM moving to the fore. A definition of agents and agent-based models is given; identifying their advantages and disadvantages, especially in relation to geospatial modelling. The potential use of agent-based models is discussed, and how-to instructions for developing an agent-based model are provided. Types of simulation / modelling systems available for ABM are defined, supplemented with criteria to consider before choosing a particular system for a modelling endeavour. Information pertaining to a selection of simulation / modelling systems (Swarm, MASON, Repast, StarLogo, NetLogo, OBEUS, AgentSheets and AnyLogic) is provided, categorised by their licensing policy (open source, shareware / freeware and proprietary systems). The evaluation (i.e. verification, calibration, validation and analysis) of agent-based models and their output is examined, and noteworthy applications are discussed.Geographical Information Systems (GIS) are a particularly useful medium for representing model input and output of a geospatial nature. However, GIS are not well suited to dynamic modelling (e.g. ABM). In particular, problems of representing time and change within GIS are highlighted. Consequently, this paper explores the opportunity of linking (through coupling or integration / embedding) a GIS with a simulation / modelling system purposely built, and therefore better suited to supporting the requirements of ABM. This paper concludes with a synthesis of the discussion that has proceeded
Mesmerizer: A Effective Tool for a Complete Peer-to-Peer Software Development Life-cycle
In this paper we present what are, in our experience, the best
practices in Peer-To-Peer(P2P) application development and
how we combined them in a middleware platform called Mesmerizer. We explain how simulation is an integral part of
the development process and not just an assessment tool.
We then present our component-based event-driven framework for P2P application development, which can be used
to execute multiple instances of the same application in a
strictly controlled manner over an emulated network layer
for simulation/testing, or a single application in a concurrent
environment for deployment purpose. We highlight modeling aspects that are of critical importance for designing and
testing P2P applications, e.g. the emulation of Network Address Translation and bandwidth dynamics. We show how
our simulator scales when emulating low-level bandwidth
characteristics of thousands of concurrent peers while preserving a good degree of accuracy compared to a packet-level
simulator
BioSimulator.jl: Stochastic simulation in Julia
Biological systems with intertwined feedback loops pose a challenge to
mathematical modeling efforts. Moreover, rare events, such as mutation and
extinction, complicate system dynamics. Stochastic simulation algorithms are
useful in generating time-evolution trajectories for these systems because they
can adequately capture the influence of random fluctuations and quantify rare
events. We present a simple and flexible package, BioSimulator.jl, for
implementing the Gillespie algorithm, -leaping, and related stochastic
simulation algorithms. The objective of this work is to provide scientists
across domains with fast, user-friendly simulation tools. We used the
high-performance programming language Julia because of its emphasis on
scientific computing. Our software package implements a suite of stochastic
simulation algorithms based on Markov chain theory. We provide the ability to
(a) diagram Petri Nets describing interactions, (b) plot average trajectories
and attached standard deviations of each participating species over time, and
(c) generate frequency distributions of each species at a specified time.
BioSimulator.jl's interface allows users to build models programmatically
within Julia. A model is then passed to the simulate routine to generate
simulation data. The built-in tools allow one to visualize results and compute
summary statistics. Our examples highlight the broad applicability of our
software to systems of varying complexity from ecology, systems biology,
chemistry, and genetics. The user-friendly nature of BioSimulator.jl encourages
the use of stochastic simulation, minimizes tedious programming efforts, and
reduces errors during model specification.Comment: 27 pages, 5 figures, 3 table
Integrated urban evolutionary modeling
Cellular automata models have proved rather popular as frameworks for simulating the physical growth of cities. Yet their brief history has been marked by a lack of application to real policy contexts, notwithstanding their obvious relevance to topical problems such as urban sprawl. Traditional urban models which emphasize transportation and demography continue to prevail despite their limitations in simulating realistic urban dynamics. To make progress, it is necessary to link CA models to these more traditional forms, focusing on the explicit simulation of the socio-economic attributes of land use activities as well as spatial interaction. There are several ways of tackling this but all are based on integration using various forms of strong and loose coupling which enable generically different models to be connected. Such integration covers many different features of urban simulation from data and software integration to internet operation, from interposing demand with the supply of urban land to enabling growth, location, and distributive mechanisms within such models to be reconciled. Here we will focus on developin
Investigating biocomplexity through the agent-based paradigm.
Capturing the dynamism that pervades biological systems requires a computational approach that can accommodate both the continuous features of the system environment as well as the flexible and heterogeneous nature of component interactions. This presents a serious challenge for the more traditional mathematical approaches that assume component homogeneity to relate system observables using mathematical equations. While the homogeneity condition does not lead to loss of accuracy while simulating various continua, it fails to offer detailed solutions when applied to systems with dynamically interacting heterogeneous components. As the functionality and architecture of most biological systems is a product of multi-faceted individual interactions at the sub-system level, continuum models rarely offer much beyond qualitative similarity. Agent-based modelling is a class of algorithmic computational approaches that rely on interactions between Turing-complete finite-state machines--or agents--to simulate, from the bottom-up, macroscopic properties of a system. In recognizing the heterogeneity condition, they offer suitable ontologies to the system components being modelled, thereby succeeding where their continuum counterparts tend to struggle. Furthermore, being inherently hierarchical, they are quite amenable to coupling with other computational paradigms. The integration of any agent-based framework with continuum models is arguably the most elegant and precise way of representing biological systems. Although in its nascence, agent-based modelling has been utilized to model biological complexity across a broad range of biological scales (from cells to societies). In this article, we explore the reasons that make agent-based modelling the most precise approach to model biological systems that tend to be non-linear and complex
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