jNeuroML is a Free/Open Source Java tool for working with LEMS and NeuroML 2.
It includes the
jnml command line application, and can also be used as a Java library.
With jNeuroML you can:
Validate NeuroML v1.8.1 and v2.x files
Simulate NeuroML 2 models
Export NeuroML 2 and LEMS files to many formats such as Neuron, Brian, Matlab, etc.
Import other languages into LEMS (e.g. SBML)
Visualise NeuroML models and simulations
pyNeuroML builds on jNeuroML and includes additional functions.
Install the Java Runtime Environment#
Since jNeuroML is written in Java, you will need a Java Runtime Environment (JRE) installed on your system. On most Linux systems Free/Open source OpenJDK runtime environment is already pre-installed. You can also install Oracle’s proprietary Java platform from their download page if you prefer. Please refer to your operating system’s documentation to install a JRE.
Installation using pre-compiled JAR#
jNeuroML is provided as a pre-compiled ready-to-use Java JAR file that can be used on any computer that has Java installed. Please download it from the GitHub release page and unzip (extract) it in a preferred folder on your computer:
cd <folder where you downloaded the jNeuroML zip file> unzip jNeuroML.zip
This will extract the zip file to a new folder which will contain the pre-compiled JAR file and runner scripts:
ls jNeuroMLJar/ jNeuroML-0.10.2-jar-with-dependencies.jar jnml jnml.bat README
Add instructions on using the installer script. NeuroML/jNeuroML#76
Installation on Fedora Linux#
On Fedora Linux systems, the NeuroFedora community provides jNeuroML as a package in their extras repository and can be installed using the following commands:
sudo dnf copr enable @neurofedora/neurofedora-extra sudo dnf install jneuroml
Information on usage of the
jnml command line application can be found with the -h option:
jnml -h jNeuroML v0.10.1 Usage: jnml LEMSFile.xml Load LEMSFile.xml using jLEMS, parse it and validate it as LEMS, and execute the model it contains jnml LEMSFile.xml -nogui As above, parse and execute the model and save results, but don't show GUI ...
The jNeuroML API is self documented. Please refer to the various packages to learn their usage:
NeuroML/jNeuroML (API Documentation here)
NeuroML/org.neuroml.model (API Documentation here)
NeuroML/org.neuroml.model.injectingplugin (API Documentation here)
NeuroML/org.neuroml.import: Import other formats into LEMS & combine with NeuroML models (API documentation here)
NeuroML/org.neuroml.export: Export from NeuroML & LEMS (API Documentation here)
For any questions regarding jNeuroML, please open an issue on the GitHub issue tracker here. Any bugs and feature requests can also be filed there.
You can also use any of the communication channels of the NeuroML community.
jNeuroML is developed on GitHub at NeuroML/jNeuroML under the LPGL-3.0 license. The repository contains the complete source code along with instructions on building/installing jNeuroML. Please follow the instructions there to build jNeuroML from source.
Nightly (pre-release) jar builds:#
Please note that these JARs are considered experimental and should only be used for testing purposes.
In case you want to use a development (un-released) version of jNeuroML, you can download a development build following the steps below. You will need to have the Subversion tool installed on your system.
svn checkout svn://svn.code.sf.net/p/neuroml/code/jNeuroMLJar cd jNeuroMLJar