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

The Spatial Variability of Vehicle Densities as Determinant of Urban Network Capacity

Due to the complexity of the traffic flow dynamics in urban road networks, most quantitative descriptions of city traffic so far are based on computer simulations. This contribution pursues a macroscopic (fluid-dynamic) simulation approach, which facilitates a simple simulation of congestion spreading in cities. First, we show that a quantization of the macroscopic turning flows into units of single vehicles is necessary to obtain realistic fluctuations in the traffic variables, and how this can be implemented in a fluid-dynamic model. Then, we propose a new method to simulate destination flows without the requirement of individual route assignments. Combining both methods allows us to study a variety of different simulation scenarios. These reveal fundamental relationships between the average flow, the average density, and the variability of the vehicle densities. Considering the inhomogeneity of traffic as an independent variable can eliminate the scattering of congested flow measurements. The variability also turns out to be a key variable of urban traffic performance. Our results can be explained through the number of full links of the road network, and approximated by a simple analytical formula

Modeling the Internet of Things: a simulation perspective

This paper deals with the problem of properly simulating the Internet of Things (IoT). Simulating an IoT allows evaluating strategies that can be employed to deploy smart services over different kinds of territories. However, the heterogeneity of scenarios seriously complicates this task. This imposes the use of sophisticated modeling and simulation techniques. We discuss novel approaches for the provision of scalable simulation scenarios, that enable the real-time execution of massively populated IoT environments. Attention is given to novel hybrid and multi-level simulation techniques that, when combined with agent-based, adaptive Parallel and Distributed Simulation (PADS) approaches, can provide means to perform highly detailed simulations on demand. To support this claim, we detail a use case concerned with the simulation of vehicular transportation systems.Comment: Proceedings of the IEEE 2017 International Conference on High Performance Computing and Simulation (HPCS 2017

Detailed simulations of cell biology with Smoldyn 2.1.

Most cellular processes depend on intracellular locations and random collisions of individual protein molecules. To model these processes, we developed algorithms to simulate the diffusion, membrane interactions, and reactions of individual molecules, and implemented these in the Smoldyn program. Compared to the popular MCell and ChemCell simulators, we found that Smoldyn was in many cases more accurate, more computationally efficient, and easier to use. Using Smoldyn, we modeled pheromone response system signaling among yeast cells of opposite mating type. This model showed that secreted Bar1 protease might help a cell identify the fittest mating partner by sharpening the pheromone concentration gradient. This model involved about 200,000 protein molecules, about 7000 cubic microns of volume, and about 75 minutes of simulated time; it took about 10 hours to run. Over the next several years, as faster computers become available, Smoldyn will allow researchers to model and explore systems the size of entire bacterial and smaller eukaryotic cells

Data-driven modelling of biological multi-scale processes

Biological processes involve a variety of spatial and temporal scales. A holistic understanding of many biological processes therefore requires multi-scale models which capture the relevant properties on all these scales. In this manuscript we review mathematical modelling approaches used to describe the individual spatial scales and how they are integrated into holistic models. We discuss the relation between spatial and temporal scales and the implication of that on multi-scale modelling. Based upon this overview over state-of-the-art modelling approaches, we formulate key challenges in mathematical and computational modelling of biological multi-scale and multi-physics processes. In particular, we considered the availability of analysis tools for multi-scale models and model-based multi-scale data integration. We provide a compact review of methods for model-based data integration and model-based hypothesis testing. Furthermore, novel approaches and recent trends are discussed, including computation time reduction using reduced order and surrogate models, which contribute to the solution of inference problems. We conclude the manuscript by providing a few ideas for the development of tailored multi-scale inference methods.Comment: This manuscript will appear in the Journal of Coupled Systems and Multiscale Dynamics (American Scientific Publishers