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Interoperability of neuroscience modeling software: current status and future directions

Interoperability of neuroscience modeling software: current status and future directions

http://www.wikidata.org/entity/Q36943359

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Towards reproducible descriptions of neuronal network models.Brian: a simulator for spiking neural networks in python Current practice in software development for computational neuroscience and how to improve it NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail neuroConstruct: a tool for modeling networks of neurons in 3D space The role of type 4 phosphodiesterases in generating microdomains of cAMP: large scale stochastic simulations Virk: an active learning-based system for bootstrapping knowledge base development in the neurosciences A federated design for a neurobiological simulation engine: the CBI federated software architecture Why are computational neuroscience and systems biology so separate?Run-time interoperability between neuronal network simulators based on the MUSIC framework Technical integration of hippocampus, Basal Ganglia and physical models for spatial navigation.PyMOOSE: Interoperable Scripting in Python for MOOSE.The connection-set algebra--a novel formalism for the representation of connectivity structure in neuronal network models.PyNN: A Common Interface for Neuronal Network Simulators.Brainlab: A Python Toolkit to Aid in the Design, Simulation, and Analysis of Spiking Neural Networks with the NeoCortical Simulator.STEPS: Modeling and Simulating Complex Reaction-Diffusion Systems with Python.Trends in programming languages for neuroscience simulations.Visualizing neuronal network connectivity with connectivity pattern tables.Vectorized algorithms for spiking neural network simulation.The layer-oriented approach to declarative languages for biological modeling.Reaction-diffusion in the NEURON simulator.libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience.Topographica: Building and Analyzing Map-Level Simulations from Python, C/C++, MATLAB, NEST, or NEURON Components.Computer modelling of epilepsy Modeling signal transduction leading to synaptic plasticity: evaluation and comparison of five models.Reproducibility in Computational Neuroscience Models and Simulations.Reproducibility and Comparability of Computational Models for Astrocyte Calcium Excitability.Large-scale modeling - a tool for conquering the complexity of the brain.Database analysis of simulated and recorded electrophysiological datasets with PANDORA's toolbox.A Component-Based Extension Framework for Large-Scale Parallel Simulations in NEURON.Interoperability in the GENESIS 3.0 Software Federation: the NEURON Simulator as an Example.Simplicity and efficiency of integrate-and-fire neuron models.Computational Models for Calcium-Mediated Astrocyte Functions.Geppetto: a reusable modular open platform for exploring neuroscience data and models

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Interoperability of neuroscience modeling software: current status and future directions

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Interoperability of neuroscience modeling software: current status and future directions

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Interoperability of neuroscience modeling software: current status and future directions

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Interoperability of neuroscience modeling software: current status and future directions

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Neuroinformatics

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Interoperability of neuroscience modeling software: current status and future directions

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Eilif Muller

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Fredrick W Howell

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Hugo Cornelis

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Joel R Stiles

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Marc-Oliver Gewaltig

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Michael L Hines

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Robert C Cannon

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Stefan Wils

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Upinder S Bhalla

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P2860

Scientific software development is not an oxymoron

Neuroscience networks: data-sharing in an information age

BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems.

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

Simulation of networks of spiking neurons: a review of tools and strategies.

Towards effective and rewarding data sharing.

MorphML: level 1 of the NeuroML standards for neuronal morphology data and model specification.

Expanding NEURON's repertoire of mechanisms with NMODL.

A sodium channel gating model based on single channel, macroscopic ionic, and gating currents in the squid giant axon

Biophysically detailed modelling of microcircuits and beyond.

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s12021-007-0004-5

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10.1007/S12021-007-0004-5

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Erik De Schutter

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2007-01-01T00:00:00Z

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5970237

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17873374

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interoperability

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2658651

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