The claustrum, a structure having extensive connectivity with the rest of the brain and being involved in many high-cognitive processes, is still one of the least understood parts of the mammalian nervous system. One of the reasons is its complex location and geometry: a folded, thin layer of neurons, sandwiched between other cellular groups and white matter tracts, which creates specific...
The 70th anniversary of the first simulation of a spiking neuronal network by Farley and Clark (Proceedings of the 1954 Symposium on Information Theory, Institute of Radio Engineers) provides a good opportunity to take stock of the development of spiking network simulations over the past seven decades, chart present practices in the field and develop perspectives for the future scientific...
NEST simulations are typically executed by a script that configures and runs the simulation. Despite recent improvements in NEST 3.x, where file headers specify the detailed origin of the outputs, users still must interpret the data with respect to the simulation setup. This information is difficult to convey, especially in collaborative contexts with shared simulation results. Moreover,...
The development and function of the cerebral cortex of the mammalian brain is a complex orchestration of cellular dynamics leading to a highly specialised structure. The present study explores the development of a gene regulatory network that abstracts the underlying DNA and genetic expression responsible for this anatomical process. An agent-based model is created in the high performance...
NEST Desktop is a web-based GUI application for NEST Simulator [1, 2]. It has been established as an useful tool to guide students and newcomers to learn the concept of computational neuroscience exploring the behavior of neuron models or network dynamics.
The latest release (v3.3) provides the more models, e.g. multi-compartmental models or even synaptic models for plasticity (STDP,...
A model for NMDA-receptor-mediated synaptic currents generating persistent activity proposed by Wang and Brunel [1-3] has been widely adopted in computational neuroscience, both for spiking-neuron and mean-field models [1-4]. The model describes synaptic dynamics by a phenomenological two-dimensional nonlinear ODE system for the gating variable S(t). Due to the nonlinearity, the pre-synaptic...
We developed a biologically grounded model of the human hippocampus CA1 region. The model includes all the pyramidal cells and interneurons with a realistic number of cells (about 5 millions) and their connections (31 billions). The connectivity matrix was generated using previously published methods [1] and stored in the SONATA data format. The model is set to run in the NEST simulator using...
NESTML is a domain-specific modeling language for neuron models and synaptic plasticity rules [1]. It is designed to support researchers in computational neuroscience by allowing them to specify models in a precise and intuitive way. These models can subsequently be used in dynamical simulations of small or large-scale spiking neural networks, using high-performance simulation code generated...
NEST, a distributed neural network simulator, is capable of simulating large, sparsely interconnected networks, wherein axons and dendrites are represented as simple transmission delays. The synapses in these networks can incorporate plasticity mechanisms, including the widely used spike-timing dependent plasticity (STDP). Presently, NEST employs purely dendritic delays, which are suitable for...
Microcircuits are the building blocks of the neocortex [1]. Single instances have been reconstructed experimentally (e.g., [2]), and their general dynamics and information processing capabilities have been investigated theoretically (e.g., [3,4]). Their connectivity is usually represented in connectivity maps consisting of probabilities that neurons establish connections. These maps reduce the...
There is mounting experimental evidence that brain-state specific neural mechanisms supported by connectomic architectures serve to combine past and contextual knowledge with current, incoming flow of evidence (e.g. from sensory systems). Such mechanisms are distributed across multiple spatial and temporal scales and require dedicated support at the levels of individual neurons and synapses. A...
