Standard Formats
Displaying: 3 Found: 18 Total: 18
Biophysics v1.8.1
NeuroML Version 1.8.1 Level 2 Biophysics
Synopsis
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
Authors
Organizations
Biological Scales
Scale | molecular | cellular | tissue | organ | organism | ecosystem |
---|---|---|---|---|---|---|
Support | intrinsic | intrinsic | unknown | unknown | unknown | unknown |
Spatial Representation
Spatial Representation Level | Compartment | Dimensions | Gradients | Spatial Structures |
---|---|---|---|---|
Support | unknown | unknown | unknown | unknown |
Advantage
- Multiscale Models
Modularity: yes
Components Relation
Flat Network:
no
Supported Math
Unit Support
Unit Required: yes
Support: intrinsic
Annotation Support
Miriram Support: no
identifiers.org Support: no
Description
Links
Specification
Webpage
Model repository
Software Repository
Full XSD
Specification
NeuroML
Description
Model Description Language for Computational Neuroscience
Derived from
Publication date
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
CellML 1.1
CellML 1.1
Synopsis
Description
CellML is an XML-based exchange format developed by the University of Auckland in collaboration with Physiome Sciences, Inc. CellML 1.1 has a component-based architecture allowing a modeller to build complex systems of models that expand and reuse previously published models. CellML Metadata is a format for encoding contextual information for a model. CellML 1.1 can be used in conjunction with CellML Metadata to provide a complete description of the structure and underlying mathematics of biological models. A repository of over 200 electrophysiological, mechanical, signal transduction, and metabolic pathway models is available at www.cellml.org.*
*( Autumn A. Cuellar et al. SIMULATION December 2003 79: 740-747, doi:10.1177/0037549703040939 )
Publication Date
Authors
Organizations
Biological Scales
Scale | molecular | cellular | tissue | organ | organism | ecosystem |
---|---|---|---|---|---|---|
Support | potential | potential | potential | potential | unknown | potential |
Spatial Representation
Spatial Representation Level | Compartment | Dimensions | Gradients | Spatial Structures |
---|---|---|---|---|
Support | intrinsic | unknown | unknown | unknown |
Advantage
- Model components reusability
- Multiscale Models
Modularity: yes
Components Relation
Flat Network:
yes
Supported Math
MathML Support: yes
Full MathML Support: no
Unit Support
Unit Required: yes
Support: intrinsic
Annotation Support
Miriram Support: yes
identifiers.org Support: yes
Description
Metadata specification is declared modulary and is not part of the main specification. Actual version is 2.0.
Links
Specification
Biological
Application
Format
|
||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CellML 1.1 |
Webpage
Specification
Model repository
Software Repository
Full XSD
CellML
Description
CellML describes mathematical models as a network of reusable components. The components harbor variables that change due to underling mathematical equations. The elements of CellML describe low level concepts, therefore CellML can be used in variety of not only biological topics.
Derived from
Publication date
Organizations
Links
Webpage
All formats for this class
CellML free to use license
Description
The following are the official terms of use for the CellML language:
Individuals may:
- (a) freely use, publish, and redistribute the CellML Format and documentation
- (b) write and sell applications which create, load, or write CellML-valid XML files
- (c) distribute or sell their own CellML-valid XML files
- (d) transmit verbatim copies of the CellML Format and documentation to any person, without restriction.
Links
License
ChannelML v1.8.1
NeuroML Version 1.8.1 Level 2 ChannelML
Synopsis
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
Authors
Organizations
Biological Scales
Scale | molecular | cellular | tissue | organ | organism | ecosystem |
---|---|---|---|---|---|---|
Support | intrinsic | intrinsic | unknown | unknown | unknown | unknown |
Spatial Representation
Spatial Representation Level | Compartment | Dimensions | Gradients | Spatial Structures |
---|---|---|---|---|
Support | unknown | unknown | unknown | unknown |
Advantage
- Multiscale Models
Modularity: yes
Components Relation
Flat Network:
no
Supported Math
MathML Support: no
Full MathML Support: no
Description
Own mathematical definitions in form of higher level abstractions. Or a freeform expression
Unit Support
Unit Required: yes
Support: intrinsic
Annotation Support
Miriram Support: no
identifiers.org Support: no
Description
Links
Specification
Webpage
Model repository
Software Repository
Full XSD
Specification
NeuroML
Description
Model Description Language for Computational Neuroscience
Derived from
Publication date
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.