Using neuroConstruct based projects

A number of the projects on the OSB are based on neuroConstruct projects (see here). neuroConstruct is used to import model elements in NeuroML (e.g. exported from a simulator or other application), can generate code for multiple simulators, and can export NeuroML in various formats.

Install the latest version of neuroConstruct

First, get the latest version of neuroConstruct. While there are binary installers available on the neuroConstruct download page, it’s best to use the latest version of this application from GitHub, as this will most likely be the version in which the projects on OSB were last saved.

Get the latest version of Git (see here for more about Git). Detailed instructions for installing neuroConstruct from source can be found here.

Install your simulator(s) of choice

More details on the simulators supported by OSB can be found here.

Get a local copy of one of the neuroConstruct based projects

Check out a local copy of one of the projects, e.g. project:granulecell

git clone https://github.com/OpenSourceBrain/GranuleCell.git

Run neuroConstruct as outlined in the installation instructions.

Go to File, then Open Project…, go to the folder you installed the project in and select GranuleCell/neuroConstruct/GranuleCell.ncx. Go to tab Generate and press Generate Cell Positions and Connections. Go to tab Export and then the tab for your chosen simulator (e.g. NEURON), press Create XXX files, then Run XXX simulation. For more details on the interaction of neuroConstruct with these simulators see here.

Get all neuroConstruct based projects on OSB

To clone all of the projects on OSB which contain neuroConstruct projects (and many others) use the checkOSB script in the osb subfolder of the neuroConstruct home directory:

cd osb
./checkOsb.sh -u (Linux/Mac)
checkOsb.bat -u  (Windows)

This will clone ~70 projects with ~20 containing neuroConstruct projects, which will be accessible under the File - Open Source Brain Project: