Standard Formats
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NeuroML 2 beta 3
NeuroML 2 beta 3
Synopsis
Description
We have developed a compact, hierarchical, XML-based language called LEMS (Low Entropy Model Specification), that can define the structure and dynamics of a wide range of biological models in a fully machine readable format. We describe how LEMS underpins the latest version of NeuroML and show that this framework can define models of ion channels, synapses, neurons and networks. Unit handling, often a source of error when reusing models, is built into the core of the language by specifying physical quantities in models in terms of the base dimensions. We show how LEMS, together with the open source Java and Python based libraries we have developed, facilitates the generation of scripts for multiple neuronal simulators and provides a route for simulator free code generation. We establish that LEMS can be used to define models from systems biology and map them to neuroscience-domain specific simulators, enabling models to be shared between these traditionally separate disciplines. LEMS and NeuroML 2 provide a new, comprehensive framework for defining computational models of neuronal and other biological systems in a machine readable format, making them more reproducible and increasing the transparency and accessibility of their underlying structure and properties.*
*(Cannon RC et al. Frontiers in Neuroinformatics. 2014;8:79. )
Publication Date
Authors
Organizations
Biological Scales
Scale | molecular | cellular | tissue | organ | organism | ecosystem |
---|---|---|---|---|---|---|
Support | intrinsic | intrinsic | intrinsic | intrinsic | unknown | unknown |
Spatial Representation
Spatial Representation Level | Compartment | Dimensions | Gradients | Spatial Structures |
---|---|---|---|---|
Support | intrinsic | intrinsic | potential | intrinsic |
Advantage
- Automated consistency checking
- Multiscale Models
- Translation from Blender
Modularity: yes
Components Relation
Flat Network:
no
Supported Math
MathML Support: no
Full MathML Support: no
Description
Uses own mathematical grammar.
Unit Support
Unit Required: yes
Support: intrinsic
Description
Annotation Support
Biological
Application
Format
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NeuroML 2 beta 3 |
NeuroML
Description
Model Description Language for Computational Neuroscience
Derived from
Publication date
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Links
Webpage
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Description
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