Current application support for NeuroML
The following is a list of software applications which currently support NeuroML (last updated: 28th May 2010). Note that not all tools support all parts of NeuroML. The level of support is generally higher for applications closer to the top of the list.
| Please contact us if you would like your application included on this list! |
| NeuroML Validator | The NeuroML Validator on this website can be used to check the validity of a NeuroML file. The validator allows you
to paste the text of the file into the browser window for validation. After validation, the NeuroML Validator allows translation of
NeuroML documents into more readable HTML formats or into simulator scripts for use with GENESIS, MOOSE, NEURON and PSICS. The website also facilitates visualisation of the contents of NeuroML files in 3D using X3D. |
| neuroConstruct | neuroConstruct is a Java based application for constructing 3D networks of biologically realistic neurons. The current version can generate code for the NEURON, GENESIS, PSICS and PyNN platforms and also provides import/export support for MorphML, ChannelML and NetworkML. A detailed description of the current support for NeuroML in neuroConstruct is avaliable here. |
| NEURON | The NEURON simulation environment is one of the main target platforms for a standard facilitating exchange of neuronal models. Version 6.1 of NEURON can import and export (from ModelView) model specifications in NeuroML format. For the latest files for importing/exporting NeuroML in NEURON see here. The NeuroML Validator can also be used to generate NEURON scripts (example) and full NEURON simulations can be generated from NeuroML components by neuroConstruct. |
| GENESIS | GENESIS is a commonly used neuronal simulation environment and is also a main target platform for the NeuroML specifications. Cell morphologies and channel mechanisms in NeuroML format can be used to generate GENESIS scripts through the NeuroML Validator page here (example). This conversion can be done with any XML tool for handling XSL file transformations, but a short script in Python to facilitate this is available here. Full GENESIS simulations can be generated from NeuroML components by neuroConstruct. |
| MOOSE | MOOSE is the Multiscale Object-Oriented Simulation Environment. It is the base and numerical core for large, detailed multi-scale simulations that span computational neuroscience and systems biology. It is based on a complete reimplementation of the GENESIS 2 core, and scripts for that environment are largely compatible with MOOSE, e.g. those generated by the NeuroML Validator (example). Native support for NeuroML in MOOSE is under development. The latest version of neuroConstruct can be used to generate executable scripts for MOOSE based on NeuroML components. |
| PSICS | PSICS is the Parallel Stochastic Ion Channel Simulator. This recently developed simulator has had an initial focus on single cell modeling, but support for networks of cells is in development. Level 1 morphologies are natively supported by PSICS for specifying cell structures. PSICS does not have an internal representation of cables, so MorphML cable elements are only used to assign labels to points, but these can then be used as targets for channel allocation much as cables are in NEURON. PSICS natively reads a large subset of channel specifications in ChannelML 1.8.1 but does not support ligand gated channels (e.g. for BK, SK channels), synapses or integrate-and-fire mechanisms. Supported ChannelML files can be converted to PSICS format using the latest XSL file for this mapping (example). This converts the XML into a PSICS compatible XML file and reports the problem if the ChannelML file uses an unsupported construct. The latest version of neuroConstruct can be used to generate executable scripts for PSICS based on NeuroML components. |
| PyNN | PyNN is a Python package for simulator independent specification of neuronal network models. Model code can be developed using the PyNN API and then run using NEURON, NEST, PCSIM, Brian or MOOSE. The developed model also can be stored as a NeuroML document using code that is currently in the testing phase. The latest version of neuroConstruct can be used to generate executable scripts for PyNN based simulators based on NeuroML components, although the majority of multicompartmental conductance based models which are available in neuroConstruct are outside the current scope of the PyNN API. |
| Whole Brain Catalog | NeuroML is one of the data formats supported by this 3D visualisation environment. Further integration with tools such as neuroConstruct is currently being tested to facilitate large scale network simulations. |
| NeuronLand | NeuronLand provides NLMorphologyConverter, which is a command line program for converting between over 20 different 3D neuron morphology formats, and NLMorphologyViewer, which provides a simple interface for viewing these data. Both provide import and export of MorphML. |
| PCSIM | PCSIM is a tool in C++ for simulating large scale networks of cells and synapses. Functionality for importing and exporting NeuroML is in development. |
| CX3D | CX3D is a tool for simulating the growth of cortex in 3D. Export of generated networks to NeuroML format is included in the current version (see here). |
| Neuromantic | Neuromantic is a freeware tool for neuronal reconstruction (similar in some ways to part of Neurolucida's functionality). Neuromantic mainly uses SWC/Cvapp format, but the latest version can import and export MorphML. |
| Neurospaces/ GENESIS 3 | The Neurospaces project is developing a modular reimplementation of the core of GENESIS 2 along with a number of other components for computational neuroscience as part of the GENESIS 3 initiative. Neurospaces/GENESIS 3 currently supports reading of passive models in NeuroML format (morphology + passive parameters). |
| NeuroML Java API | A Java API generated from NeuroML schemas to be used for the development of new neural simulators and to connect with pre-existing simulators. This application has been recently updated to use Schemas from NeuroML version 1.8.1. |
Planning support for NeuroML...
The following is a list of software applications which have included NeuroML support in their development roadmaps.
Please contact the developers directly to enquire about the latest status, or with offers to help test (or implement...) NeuroML support.
| NETMORPH | NETMORPH is a simulation environment for the developmental generation of 3D large-scale neuronal networks with realistic neuron morphologies. Export of generated cells and networks into NeuroML formats is planned in future versions. |
| NeuronStudio | Free neuronal reconstruction software from the Computational Neurobiology and Imaging Center at Mount Sinai School of Medicine. Support for MorphML export is planned for future releases. |
| Neuroptikon | Neuroptikon is a tool for visualizing and interacting with neural circuits and other types of networks, being developed at Janelia Farm. Support for importing cells and networks expressed in NeuroML is planned for future releases. |