Standard Formats

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NeuroML 2 beta 3


NeuroML 2 beta 3

Synopsis

NeuroML 2 is a LEMS (Low Entropy Model Specification) based format, that can define models of ion channels, synapses, neurons and networks.

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

09/2014

Authors

Gleeson, Padraig
C. Cannon, Robert
Crook, Sharon
Silver, Angus
Ganapathy, Gautham
Marin, Boris
Piasini, Eugenio

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

Modeling Formalisms for this format

Software support for this format

Examples for this format


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

Intrinsic unit checking

Annotation Support


Java API for NeuroML 2


Programming language

Java

Links

API

PyLEMS


Programming language

Python

Links

API

libNeuroML


Programming language

Python

Links

jNeuroML


Programming language

Java

Links

Software

jNeuroML


NeuroML


Description

Model Description Language for Computational Neuroscience

Derived from

XML, LEMS

Publication date

08/2001

Organizations

Links

Webpage

All formats for this class

not defined


Description

The licence agreement is not defined or could not be obtained.