jNeuroML

There are a number of repositories in active development under GitHub for handling NeuroML and LEMS with Java. To make it easier to access all of this functionality, we've created a single package, jNeuroML, which allows access to most of this functionality through a simple command line interface and requires minimal installation.

jNeuroML can:

• Validate NeuroML v1.8.1 and v2.x files
• Simulate most NeuroML 2 models (simulation should be specificed in Simulation element in LEMS file)
• Export NeuroML 2 and LEMS to many formats such as Neuron, Brian, Matlab, etc.
• Import other languages into LEMS (e.g. SBML)

Binary installation

To get a precompiled binary for jNeuroML:

1. Go to https://github.com/NeuroML/jNeuroML/releases and download the latest jNeuroML.zip file
2. Unzip it to your local machine
3. Add environment variable JNML_HOME, pointing to the root jNeuroML folder
4. Add the location of the jNeuroML folder to the PATH variable. This and the previous step will ensure you can run the jnml utility from any folder.

Usage

Typing ./jnml (or jnml.bat on Windows) will list the options available. Some of the current options include:

./jnml -validate MyNeuroML.nml              (validate NeuroML 2 document against the current schema)
./jnml -validatev1 MyNeuroML1.xml           (validate NeuroML v1 document against the v1.8.1 schema)
./jnml MyLEMS.xml                           (parse & simulate a LEMS model using jLEMS)
./jnml MyLEMS.xml -graph                    (generate png of structure of LEMS model using GraphViz)
./jnml MyLEMS.xml -neuron                   (generate code to run on the NEURON simulator)

Export and import features for NEURON, SBML, Brian etc. are under active development (see https://github.com/NeuroML/org.neuroml.export and https://github.com/NeuroML/org.neuroml.import).

Getting the source for jNeuroML

If you prefer to clone all of the individual repositories and build the jNeuroML application yourself, use the getNeuroML.py utility in the jNeuroML repo.

Eensure you have:

• git
• Java Development Kit (JDK) and JAVA_HOME variable set (see here for Ubuntu).
• Maven: Download here or use package managers for Linux (e.g. sudo apt-get install maven) or Mac (brew install maven).

Then in terminal, run:

git clone git://github.com/NeuroML/jNeuroML.git neuroml_dev/jNeuroML
cd neuroml_dev/jNeuroML
python getNeuroML.py

This will clone ~11 repos for NML2 & LEMS (including Python based libraries) into neuroml_dev/ and compile the Java based ones using Maven. The full process may take 5-10 mins on first installation, but subsequently running:

git pull
python getNeuroML.py

in the jNeuroML folder will get the stable version of each repo & compile using Maven if necessary.

To access the very latest version (the development branches of the GitHub repos) use:

python getNeuroML.py clean
python getNeuroML.py development

Use of Maven is a great way to manage versions of applications being developed in distributed repositories, and will make it easy to use selected parts of this for different Java applications. For example, these packages will be used in various ways to provide NeuroML/LEMS support in neuroConstruct and for handling NeuroML on the Open Source Brain website.

Prefer Python?

If you prefer using/installing/coding in Python, try out pyNeuroML. Much of the functionality of jNeuroML is bundled inside pyNeuroML and can be accessed with a command line utility (pynml) with similar usage as jnml.

This code is distributed under the terms of the GNU Lesser General Public License.