321 research outputs found
GeNN: a code generation framework for accelerated brain simulations
Large-scale numerical simulations of detailed brain circuit models are important for identifying hypotheses on brain functions and testing their consistency and plausibility. An ongoing challenge for simulating realistic models is, however, computational speed. In this paper, we present the GeNN (GPU-enhanced Neuronal Networks) framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale neuronal networks to address this challenge. GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs, through a flexible and extensible interface, which does not require in-depth technical knowledge from the users. We present performance benchmarks showing that 200-fold speedup compared to a single core of a CPU can be achieved for a network of one million conductance based Hodgkin-Huxley neurons but that for other models the speedup can differ.
GeNN is available for Linux, Mac OS X and Windows platforms. The source code, user manual, tutorials,
Wiki, in-depth example projects and all other related information can be found on the project website http://genn-team.github.io/genn/
DAMNED: A Distributed and Multithreaded Neural Event-Driven simulation framework
In a Spiking Neural Networks (SNN), spike emissions are sparsely and
irregularly distributed both in time and in the network architecture. Since a
current feature of SNNs is a low average activity, efficient implementations of
SNNs are usually based on an Event-Driven Simulation (EDS). On the other hand,
simulations of large scale neural networks can take advantage of distributing
the neurons on a set of processors (either workstation cluster or parallel
computer). This article presents DAMNED, a large scale SNN simulation framework
able to gather the benefits of EDS and parallel computing. Two levels of
parallelism are combined: Distributed mapping of the neural topology, at the
network level, and local multithreaded allocation of resources for simultaneous
processing of events, at the neuron level. Based on the causality of events, a
distributed solution is proposed for solving the complex problem of scheduling
without synchronization barrier.Comment: 6 page
ARACHNE: A neural-neuroglial network builder with remotely controlled parallel computing
Creating and running realistic models of neural networks has hitherto been a task for computing professionals rather than experimental neuroscientists. This is mainly because such networks usually engage substantial computational resources, the handling of which requires specific programing skills. Here we put forward a newly developed simulation environment ARACHNE: it enables an investigator to build and explore cellular networks of arbitrary biophysical and architectural complexity using the logic of NEURON and a simple interface on a local computer or a mobile device. The interface can control, through the internet, an optimized computational kernel installed on a remote computer cluster. ARACHNE can combine neuronal (wired) and astroglial (extracellular volume-transmission driven) network types and adopt realistic cell models from the NEURON library. The program and documentation (current version) are available at GitHub repository https://github.com/LeonidSavtchenko/Arachne under the MIT License (MIT)
Memory and information processing in neuromorphic systems
A striking difference between brain-inspired neuromorphic processors and
current von Neumann processors architectures is the way in which memory and
processing is organized. As Information and Communication Technologies continue
to address the need for increased computational power through the increase of
cores within a digital processor, neuromorphic engineers and scientists can
complement this need by building processor architectures where memory is
distributed with the processing. In this paper we present a survey of
brain-inspired processor architectures that support models of cortical networks
and deep neural networks. These architectures range from serial clocked
implementations of multi-neuron systems to massively parallel asynchronous ones
and from purely digital systems to mixed analog/digital systems which implement
more biological-like models of neurons and synapses together with a suite of
adaptation and learning mechanisms analogous to the ones found in biological
nervous systems. We describe the advantages of the different approaches being
pursued and present the challenges that need to be addressed for building
artificial neural processing systems that can display the richness of behaviors
seen in biological systems.Comment: Submitted to Proceedings of IEEE, review of recently proposed
neuromorphic computing platforms and system
A Novel GPU-Enabled Simulator for Large Scale Spiking Neural Networks, Journal of Telecommunications and Information Technology, 2016, nr 2
e understanding of the structural and dynamic complexity of neural networks is greatly facilitated by computer simulations. An ongoing challenge for simulating realistic models is, however, computational speed. In this paper a framework for modeling and parallel simulation of biological-inspired large scale spiking neural networks on high-performance graphics processors is described. This tool is implemented in the OpenCL programming technology. It enables simulation study with three models: Integrate-andfire, Hodgkin-Huxley and Izhikevich neuron model. The results of extensive simulations are provided to illustrate the operation and performance of the presented software framework. The particular attention is focused on the computational speed-up factor
Why Are Computational Neuroscience and Systems Biology So Separate?
Despite similar computational approaches, there is surprisingly little interaction between the computational neuroscience and the systems biology research communities. In this review I reconstruct the history of the two disciplines and show that this may explain why they grew up apart. The separation is a pity, as both fields can learn quite a bit from each other. Several examples are given, covering sociological, software technical, and methodological aspects. Systems biology is a better organized community which is very effective at sharing resources, while computational neuroscience has more experience in multiscale modeling and the analysis of information processing by biological systems. Finally, I speculate about how the relationship between the two fields may evolve in the near future
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