Standard Formats

Displaying: 1 Found: 1 Total: 18


NetworkML v1.8.1


NeuroML Version 1.8.1 Level 3 NetworkML

Synopsis

Describing cell placement and network connectivity.

Description

Biologically detailed single neuron and network models are important for understanding how ion channels, synapses and anatomical connectivity underlie the complex electrical behavior of the brain. [...] We have used an Open Source software approach to develop NeuroML, a neuronal model description language based on XML (Extensible Markup Language). This enables these detailed models and their components to be defined in a standalone form, allowing them to be used across multiple simulators and archived in a standardized format. Here we describe the structure of NeuroML and demonstrate its scope by converting into NeuroML models of a number of different voltage- and ligand-gated conductances, models of electrical coupling, synaptic transmission and short-term plasticity, together with morphologically detailed models of individual neurons. We have also used these NeuroML-based components to develop an highly detailed cortical network model. NeuroML-based model descriptions were validated by demonstrating similar model behavior across five independently developed simulators. Although our results confirm that simulations run on different simulators converge, they reveal limits to model interoperability, by showing that for some models convergence only occurs at high levels of spatial and temporal discretisation, when the computational overhead is high. Our development of NeuroML as a common description language for biophysically detailed neuronal and network models enables interoperability across multiple simulation environments, thereby improving model transparency, accessibility and reuse in computational neuroscience.*

*(Gleeson P et al. PLoS Computational Biology. 2010;6(6))

Publication Date

06/2009

Authors

Gleeson, Padraig
C. Cannon, Robert
Crook, Sharon
L. Hines, Michael
O. Billings, Guy
Farinella, Matteo
M. Morse, Thomas
P. Davison, Andrew
Ray, Subhasis
S. Bhalla, Upinder
R. Barnes, Simon
D. Dimitrova, Yoana
Silver, Angus

Organizations


Biological Scales

Scale molecular cellular tissue organ organism ecosystem
Support unknown unknown intrinsic intrinsic unknown unknown

Spatial Representation

Spatial Representation Level Compartment Dimensions Gradients Spatial Structures
Support intrinsic intrinsic unknown intrinsic

Modeling Formalisms for this format

Software support for this format

Examples for this format


Advantage

  • Multiscale Models

Modularity: yes


Components Relation
Flat Network: no


Supported Math


Unit Support

Unit Required: yes

Support: intrinsic

Description

length units requiered

Annotation Support

Miriram Support: no

identifiers.org Support: no

Description

Any kind of XML elements can be used inside the annotation element. Metadata has its own specification.

Links

Specification


There are no transformations available!

neuroml-api


Programming language

Java

Links

jNeuroML


Programming language

Java

Links

Software

NeuroML


Validation Portal

NeuroML


Description

Model Description Language for Computational Neuroscience

Derived from

XML, LEMS

Publication date

08/2001

Organizations

Links

Webpage

All formats for this class

GNU General Public License, version 2


Description

Free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation.

For detailed information see webpage.

Links