PyNN
The PyNN API aims to support modelling at a high-level of abstraction (populations of neurons, layers, columns and the connections between them) while still allowing access to the details of individual neurons and synapses when required. PyNN provides a library of standard neuron, synapse and synaptic plasticity models, which have been verified to work the same on the different supported simulators. PyNN also provides a set of commonly-used connectivity algorithms (e.g. all-to-all, random, distance-dependent, small-world) but makes it easy to provide your own connectivity in a simulator-independent way, either using the Connection Set Algebra or by writing your own Python code. PyNN has been developed as a procedural description in Python which can be used to instantiate a network across multiple simulators.
Description
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The PyNN API aims to support modelling at a high-level of abstraction (populations of neurons, layers, columns and the connections between them) while still allowing access to the details of individual neurons and synapses when required. PyNN provides a library of standard neuron, synapse and synaptic plasticity models, which have been verified to work the same on the different supported simulators. PyNN also provides a set of commonly-used connectivity algorithms (e.g. all-to-all, random, distance-dependent, small-world) but makes it easy to provide your own connectivity in a simulator-independent way, either using the Connection Set Algebra or by writing your own Python code. PyNN has been developed as a procedural description in Python which can be used to instantiate a network across multiple simulators.
metasource: Fairsharing.orgversion: FAIRsharing.org: PyNN; PyNN; DOI: https://doi.org/10.25504/FAIRsharing.3CCrPF; Last edited: April 16, 2021, 3:01 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Webpage:
https://neuralensemble.org/PyNN/Webpage
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https://neuralensemble.org/PyNN/
metasource: Fairsharing.orgversion: FAIRsharing.org: PyNN; PyNN; DOI: https://doi.org/10.25504/FAIRsharing.3CCrPF; Last edited: April 16, 2021, 3:01 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
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Name: CeCILLLicence name
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CeCILL
metasource: Fairsharing.orgversion: FAIRsharing.org: PyNN; PyNN; DOI: https://doi.org/10.25504/FAIRsharing.3CCrPF; Last edited: April 16, 2021, 3:01 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Licence URL
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http://www.cecill.info/licences.en.html
metasource: Fairsharing.orgversion: FAIRsharing.org: PyNN; PyNN; DOI: https://doi.org/10.25504/FAIRsharing.3CCrPF; Last edited: April 16, 2021, 3:01 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Publications:
Publications
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PyNN: A Common Interface for Neuronal Network Simulators
PMID: 19194529
metasource: Fairsharing.org
version: FAIRsharing.org: PyNN; PyNN; DOI: https://doi.org/10.25504/FAIRsharing.3CCrPF; Last edited: April 16, 2021, 3:01 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Publications
More detailed information about this field from each metasource.
PyNN: A Common Interface for Neuronal Network Simulators
PMID: 19194529
metasource: Fairsharing.org
version: FAIRsharing.org: PyNN; PyNN; DOI: https://doi.org/10.25504/FAIRsharing.3CCrPF; Last edited: April 16, 2021, 3:01 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
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PyNN: A Common Interface for Neuronal Network Simulators
PubMed citations: 170.
170 articles citing: PyNN: A Common Interface for Neuronal Network Simulators
A System-on-Chip Based Hybrid Neuromorphic Compute Node Architecture for Reproducible Hyper-Real-Time Simulations of Spiking Neural Networks. PMID:35846779
Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows. PMID:35792600
Brain-Inspired Spiking Neural Network Controller for a Neurorobotic Whisker System. PMID:35770277
Benchmarking Neuromorphic Hardware and Its Energy Expenditure. PMID:35720731
EDEN: A High-Performance, General-Purpose, NeuroML-Based Neural Simulator. PMID:35669596
A Scalable Approach to Modeling on Accelerated Neuromorphic Hardware. PMID:35663548
Parallelization of Neural Processing on Neuromorphic Hardware. PMID:35620669
Cortical oscillations support sampling-based computations in spiking neural networks. PMID:35324886
ConGen-A Simulator-Agnostic Visual Language for Definition and Generation of Connectivity in Large and Multiscale Neural Networks. PMID:35069166
PymoNNto: A Flexible Modular Toolbox for Designing Brain-Inspired Neural Networks. PMID:34790108
Spontaneous traveling waves naturally emerge from horizontal fiber time delays and travel through locally asynchronous-irregular states. PMID:34663796
The EBRAINS NeuroFeatureExtract: An Online Resource for the Extraction of Neural Activity Features From Electrophysiological Data. PMID:34512300
SyNC, a Computationally Extensive and Realistic Neural Net to Identify Relative Impacts of Synaptopathy Mechanisms on Glutamatergic Neurons and Their Networks in Autism and Complex Neurological Disorders. PMID:34354570
Event-Based Update of Synapses in Voltage-Based Learning Rules. PMID:34177505
Towards a Bio-Inspired Real-Time Neuromorphic Cerebellum. PMID:34135732
Embedding optimization reveals long-lasting history dependence in neural spiking activity. PMID:34061837
PyGeNN: A Python Library for GPU-Enhanced Neural Networks. PMID:33967731
Temporal constrained objects for modelling neuronal dynamics. PMID:33816812
Accelerating with FlyBrainLab the discovery of the functional logic of the Drosophila brain in the connectomic and synaptomic era. PMID:33616035
HippoUnit: A software tool for the automated testing and systematic comparison of detailed models of hippocampal neurons based on electrophysiological data. PMID:33513130
A New Spiking Convolutional Recurrent Neural Network (SCRNN) With Applications to Event-Based Hand Gesture Recognition. PMID:33324153
Brain Modeling ToolKit: An open source software suite for multiscale modeling of brain circuits. PMID:33253147
HFNet: A CNN Architecture Co-designed for Neuromorphic Hardware With a Crossbar Array of Synapses. PMID:33192236
Nengo and Low-Power AI Hardware for Robust, Embedded Neurorobotics. PMID:33162886
A system hierarchy for brain-inspired computing. PMID:33057220
Experimental and Computational Study on Motor Control and Recovery After Stroke: Toward a Constructive Loop Between Experimental and Virtual Embodied Neuroscience. PMID:32733210
Self-Tuning Deep Brain Stimulation Controller for Suppression of Beta Oscillations: Analytical Derivation and Numerical Validation. PMID:32694975
NeuroConstruct-based implementation of structured-light stimulated retinal circuitry. PMID:32580768
Editorial: Spiking Neural Network Learning, Benchmarking, Programming and Executing. PMID:32351350
The open EEGLAB portal Interface: High-Performance computing with EEGLAB. PMID:32289453
Simulation of Closed-Loop Deep Brain Stimulation Control Schemes for Suppression of Pathological Beta Oscillations in Parkinson's Disease. PMID:32194372
Propagating Activity in Neocortex, Mediated by Gap Junctions and Modulated by Extracellular Potassium. PMID:32098762
The SONATA data format for efficient description of large-scale network models. PMID:32092054
An efficient analytical reduction of detailed nonlinear neuron models. PMID:31941884
Real-time cortical simulation on neuromorphic hardware. PMID:31865885
Accelerated Physical Emulation of Bayesian Inference in Spiking Neural Networks. PMID:31798400
Unique Features of Network Bursts Emerge From the Complex Interplay of Excitatory and Inhibitory Receptors in Rat Neocortical Networks. PMID:31555093
Curated Model Development Using NEUROiD: A Web-Based NEUROmotor Integration and Design Platform. PMID:31440153
Brian 2, an intuitive and efficient neural simulator. PMID:31429824
Making BREAD: Biomimetic Strategies for Artificial Intelligence Now and in the Future. PMID:31316340
Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits. PMID:31201122
Reconstruction and Simulation of a Scaffold Model of the Cerebellar Network. PMID:31156416
NetPyNE, a tool for data-driven multiscale modeling of brain circuits. PMID:31025934
SpiNNTools: The Execution Engine for the SpiNNaker Platform. PMID:30971873
An unsupervised neuromorphic clustering algorithm. PMID:30944983
A Spiking Neural Network Model of Depth from Defocus for Event-based Neuromorphic Vision. PMID:30842458
BindsNET: A Machine Learning-Oriented Spiking Neural Networks Library in Python. PMID:30631269
Reproducible Neural Network Simulations: Statistical Methods for Model Validation on the Level of Network Activity Data. PMID:30618696
GPUs Outperform Current HPC and Neuromorphic Solutions in Terms of Speed and Energy When Simulating a Highly-Connected Cortical Model. PMID:30618570
Large-Scale Neuromorphic Spiking Array Processors: A Quest to Mimic the Brain. PMID:30559644
Computational neuroscience and neuroinformatics: Recent progress and resources. PMID:30541962
CABots and Other Neural Agents. PMID:30534068
Xolotl: An Intuitive and Approachable Neuron and Network Simulator for Research and Teaching. PMID:30534067
Rigorous Neural Network Simulations: A Model Substantiation Methodology for Increasing the Correctness of Simulation Results in the Absence of Experimental Validation Data. PMID:30534066
sPyNNaker: A Software Package for Running PyNN Simulations on SpiNNaker. PMID:30524220
Code Generation in Computational Neuroscience: A Review of Tools and Techniques. PMID:30455637
Replicability or reproducibility? On the replication crisis in computational neuroscience and sharing only relevant detail. PMID:30377880
A Scalable FPGA Architecture for Randomly Connected Networks of Hodgkin-Huxley Neurons. PMID:30356803
A simple decision to move in response to touch reveals basic sensory memory and mechanisms for variable response times. PMID:30074236
BioNet: A Python interface to NEURON for modeling large-scale networks. PMID:30071069
Structural Plasticity on the SpiNNaker Many-Core Neuromorphic System. PMID:30034320
Spiking neurons with short-term synaptic plasticity form superior generative networks. PMID:30006554
Spiking neural networks for computer vision. PMID:29951187
Performance Comparison of the Digital Neuromorphic Hardware SpiNNaker and the Neural Network Simulation Software NEST for a Full-Scale Cortical Microcircuit Model. PMID:29875620
Transformation of a Spatial Map across the Hippocampal-Lateral Septal Circuit. PMID:29779942
Challenges in Reproducibility, Replicability, and Comparability of Computational Models and Tools for Neuronal and Glial Networks, Cells, and Subcellular Structures. PMID:29765315
Credibility, Replicability, and Reproducibility in Simulation for Biomedicine and Clinical Applications in Neuroscience. PMID:29713272
An FPGA-Based Massively Parallel Neuromorphic Cortex Simulator. PMID:29692702
Arkheia: Data Management and Communication for Open Computational Neuroscience. PMID:29556187
Neuromodulated Synaptic Plasticity on the SpiNNaker Neuromorphic System. PMID:29535600
Binary Associative Memories as a Benchmark for Spiking Neuromorphic Hardware. PMID:28878642
A Spiking Neural Network Model of the Lateral Geniculate Nucleus on the SpiNNaker Machine. PMID:28848380
Software for Brain Network Simulations: A Comparative Study. PMID:28775687
Proprioceptive Feedback through a Neuromorphic Muscle Spindle Model. PMID:28659756
Integration of Continuous-Time Dynamics in a Spiking Neural Network Simulator. PMID:28596730
Constructing Neuronal Network Models in Massively Parallel Environments. PMID:28559808
Toward standard practices for sharing computer code and programs in neuroscience. PMID:28542156
ARACHNE: A neural-neuroglial network builder with remotely controlled parallel computing. PMID:28362877
Connecting Artificial Brains to Robots in a Comprehensive Simulation Framework: The Neurorobotics Platform. PMID:28179882
Benchmarking Spike-Based Visual Recognition: A Dataset and Evaluation. PMID:27853419
SpineCreator: a Graphical User Interface for the Creation of Layered Neural Models. PMID:27628934
pypet: A Python Toolkit for Data Management of Parameter Explorations. PMID:27610080
Simulation Neurotechnologies for Advancing Brain Research: Parallelizing Large Networks in NEURON. PMID:27557104
Deep Artificial Neural Networks and Neuromorphic Chips for Big Data Analysis: Pharmaceutical and Bioinformatics Applications. PMID:27529225
Handling Metadata in a Neurophysiology Laboratory. PMID:27486397
Modeling the Cerebellar Microcircuit: New Strategies for a Long-Standing Issue. PMID:27458345
BluePyOpt: Leveraging Open Source Software and Cloud Infrastructure to Optimise Model Parameters in Neuroscience. PMID:27375471
Building the Ferretome. PMID:27242503
Push-Pull Receptive Field Organization and Synaptic Depression: Mechanisms for Reliably Encoding Naturalistic Stimuli in V1. PMID:27242445
Empirical Bayesian significance measure of neuronal spike response. PMID:27209433
PyRhO: A Multiscale Optogenetics Simulation Platform. PMID:27148037
Reproducibility in Computational Neuroscience Models and Simulations. PMID:27046845
NeuroFlow: A General Purpose Spiking Neural Network Simulation Platform using Customizable Processors. PMID:26834542
Comparing Neuromorphic Solutions in Action: Implementing a Bio-Inspired Solution to a Benchmark Classification Task on Three Parallel-Computing Platforms. PMID:26778950
Neurokernel: An Open Source Platform for Emulating the Fruit Fly Brain. PMID:26751378
GeNN: a code generation framework for accelerated brain simulations. PMID:26740369
Integrating Visualizations into Modeling NEST Simulations. PMID:26733860
Benchmarking neuromorphic systems with Nengo. PMID:26539076
NeuroManager: a workflow analysis based simulation management engine for computational neuroscience. PMID:26528175
Impact of sub and supra-threshold adaptation currents in networks of spiking neurons. PMID:26400658
Scalability of Asynchronous Networks Is Limited by One-to-One Mapping between Effective Connectivity and Correlations. PMID:26325661
ANNarchy: a code generation approach to neural simulations on parallel hardware. PMID:26283957
Robustness of spiking Deep Belief Networks to noise and reduced bit precision of neuro-inspired hardware platforms. PMID:26217169
Network-timing-dependent plasticity. PMID:26106298
Breaking the millisecond barrier on SpiNNaker: implementing asynchronous event-based plastic models with microsecond resolution. PMID:26106288
Python in neuroscience. PMID:25926788
ModelView for ModelDB: Online Presentation of Model Structure. PMID:25896640
Probabilistic inference in discrete spaces can be implemented into networks of LIF neurons. PMID:25729361
A framework for plasticity implementation on the SpiNNaker neural architecture. PMID:25653580
Neural ensemble communities: open-source approaches to hardware for large-scale electrophysiology. PMID:25528614
Response-dependent dynamics of cell-specific inhibition in cortical networks in vivo. PMID:25504329
Spiking network simulation code for petascale computers. PMID:25346682
LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2. PMID:25309419
Limits to high-speed simulations of spiking neural networks using general-purpose computers. PMID:25309418
Characterization and compensation of network-level anomalies in mixed-signal neuromorphic modeling platforms. PMID:25303102
PyNCS: a microkernel for high-level definition and configuration of neuromorphic electronic systems. PMID:25232314
NEVESIM: event-driven neural simulation framework with a Python interface. PMID:25177291
Mechanisms of sharp wave initiation and ripple generation. PMID:25143618
A flexible, interactive software tool for fitting the parameters of neuronal models. PMID:25071540
Connection-type-specific biases make uniform random network models consistent with cortical recordings. PMID:24944218
Real-time million-synapse simulation of rat barrel cortex. PMID:24910593
Engineering a thalamo-cortico-thalamic circuit on SpiNNaker: a preliminary study toward modeling sleep and wakefulness. PMID:24904294
Supervised learning with decision margins in pools of spiking neurons. PMID:24862859
Efficient generation of connectivity in neuronal networks from simulator-independent descriptions. PMID:24795620
libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience. PMID:24795618
Python-based geometry preparation and simulation visualization toolkits for STEPS. PMID:24782754
The stimulus-evoked population response in visual cortex of awake monkey is a propagating wave. PMID:24770473
The hippocampus, medial prefrontal cortex, and selective memory retrieval: evidence from a rodent model of the retrieval-induced forgetting effect. PMID:24753146
Neo: an object model for handling electrophysiology data in multiple formats. PMID:24600386
morphforge: a toolbox for simulating small networks of biologically detailed neurons in Python. PMID:24478690
N2A: a computational tool for modeling from neurons to algorithms. PMID:24478635
A neuromorphic network for generic multivariate data classification. PMID:24469794
Current practice in software development for computational neuroscience and how to improve it. PMID:24465191
Nengo: a Python tool for building large-scale functional brain models. PMID:24431999
Neural system prediction and identification challenge. PMID:24399966
Integrated workflows for spiking neuronal network simulations. PMID:24368902
From model specification to simulation of biologically constrained networks of spiking neurons. PMID:24253973
The Convallis rule for unsupervised learning in cortical networks. PMID:24204224
Neural Schematics as a unified formal graphical representation of large-scale Neural Network Structures. PMID:24167490
Reward-based learning under hardware constraints-using a RISC processor embedded in a neuromorphic substrate. PMID:24065877
Anisotropic connectivity implements motion-based prediction in a spiking neural network. PMID:24062680
Finding a roadmap to achieve large neuromorphic hardware systems. PMID:24058330
BrainNet Viewer: a network visualization tool for human brain connectomics. PMID:23861951
Six networks on a universal neuromorphic computing substrate. PMID:23423583
Three tools for the real-time simulation of embodied spiking neural networks using GPUs. PMID:23274962
Population rate dynamics and multineuron firing patterns in sensory cortex. PMID:23197704
Supercomputers ready for use as discovery machines for neuroscience. PMID:23129998
Is a 4-bit synaptic weight resolution enough? - constraints on enabling spike-timing dependent plasticity in neuromorphic hardware. PMID:22822388
Neuronvisio: A Graphical User Interface with 3D Capabilities for NEURON. PMID:22685429
The layer-oriented approach to declarative languages for biological modeling. PMID:22615554
Emergent Auditory Feature Tuning in a Real-Time Neuromorphic VLSI System. PMID:22347163
Python as a federation tool for GENESIS 3.0. PMID:22276101
A federated design for a neurobiological simulation engine: the CBI federated software architecture. PMID:22242154
Stable learning in stochastic network states. PMID:22219282
An efficient simulation environment for modeling large-scale cortical processing. PMID:22007166
Democratic population decisions result in robust policy-gradient learning: a parametric study with GPU simulations. PMID:21572529
Context-dependent encoding of fear and extinction memories in a large-scale network model of the basal amygdala. PMID:21437238
Topologically invariant macroscopic statistics in balanced networks of conductance-based integrate-and-fire neurons. PMID:21222148
Gating of signal propagation in spiking neural networks by balanced and correlated excitation and inhibition. PMID:21106815
Compensating Inhomogeneities of Neuromorphic VLSI Devices Via Short-Term Synaptic Plasticity. PMID:21031027
NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. PMID:20585541
Functional consequences of correlated excitatory and inhibitory conductances in cortical networks. PMID:20490645
Trends in programming languages for neuroscience simulations. PMID:20198154
Visualizing neuronal network connectivity with connectivity pattern tables. PMID:20140265
The brian simulator. PMID:20011141
Reliable recall of spontaneous activity patterns in cortical networks. PMID:19923292
Towards reproducible descriptions of neuronal network models. PMID:19662159
Establishing a novel modeling tool: a python-based interface for a neuromorphic hardware system. PMID:19562085
PCSIM: A Parallel Simulation Environment for Neural Circuits Fully Integrated with Python. PMID:19543450
PyNEST: A Convenient Interface to the NEST Simulator. PMID:19198667
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network model
metasource: Fairsharing.org
version: FAIRsharing.org: PyNN; PyNN; DOI: https://doi.org/10.25504/FAIRsharing.3CCrPF; Last edited: April 16, 2021, 3:01 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
network simulation
metasource: Fairsharing.org
version: FAIRsharing.org: PyNN; PyNN; DOI: https://doi.org/10.25504/FAIRsharing.3CCrPF; Last edited: April 16, 2021, 3:01 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Tags
More detailed information about this field from each metasource.
network model
metasource: Fairsharing.orgversion: FAIRsharing.org: PyNN; PyNN; DOI: https://doi.org/10.25504/FAIRsharing.3CCrPF; Last edited: April 16, 2021, 3:01 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
network simulation
metasource: Fairsharing.orgversion: FAIRsharing.org: PyNN; PyNN; DOI: https://doi.org/10.25504/FAIRsharing.3CCrPF; Last edited: April 16, 2021, 3:01 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
network model network simulation
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