NeuroML Version 2.0

Mapping NeuroML & LEMS to other simulators and output formats


A key requirement in the development of NeuroML 2 was making it easier to map the model elements to other formats, not only to dedicated neuronal simulators, but to other generic numerical solvers and even graphical formats to increase accessibility of the model structure and dynamics. This is enabled by having access to the model definitions in a machine readable form using LEMS.

Mapping to other formats

This figure (taken from Cannon et al. 2014) shows illustrates how biological models at different physical scales and with varying levels of biological realism can be mapped into representations in LEMS. This mapping to LEMS can be made through the use of predefined, domain specific ComponentType definitions (e.g. for NeuroML 2) or by importing from other structured modelling formats (e.g. SBML). Files in LEMS can then be simulated with the reference implementations, jLEMS or PyLEMS, or exported to a number of other formats. jNeuroML is a collection of utilities in Java for handling these transformations. Export formats include neuronal simulators NEURON and Brian, MATLAB or C code for simulating the models with solvers in these languages, Modelica, XPP and SBML.

 

NEURON

A wide range of single cells (abstract to multicompartmental), networks and non NeuroML LEMS models can be mapped to NEURON (hoc and mod files).

A LEMS or NeuroML 2 model can be mapped to this format with jNeuroML using:

jnml LEMS_MyModel.xml -neuron [-nogui] [-run]

The Java source for this mapping is here (active development version).

 

SBML

There is a mapping of LEMS Components to SBML. This currently focuses on single Components (potentially in a population of size 1 in a network), since there is not yet support for arrays of compartments in the core of SBML.

A LEMS or NeuroML 2 model can be mapped to this format with jNeuroML using:

jnml LEMS_MyModel.xml -sbml

SBML models can be imported into LEMS format using:

jnml -sbml-import SBMLFile.sbml duration dt

The Java source for the export to SBML is here (active development version). Import of SBML to LEMS is here (active development version)

 

Brian

There is a mapping of LEMS Components to Brian. This currently focuses on single Components.

A LEMS or NeuroML 2 model can be mapped to this format with jNeuroML using:

jnml LEMS_MyModel.xml -brian

The Java source for this mapping is here (active development version).

 

Other formats

A full list of export formats using jNeuroML can be found with:

jnml -help

The Java source for all these mapping is here and here.


How do I convert my models to NeuroML 2?


Some pointers for converting models to NeuroML 2 can be found on the OpenSource Brain website here.

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