Requirements

neuroConstruct has been tested on on WinXP/NT, Red Hat Linux and SUSE and Mac OS. Details of the interaction with NEURON/GENESIS in each of these environments is available here. The application will run successfully on Vista too, but there is more interaction from the operating system security features (see note below).

neuroConstruct will run on most machines with a video card and which can run Java and Java3D. For networks/cells with >5000 total segments, you'll need a fairly modern machine, and the more RAM and graphics memory, the better; 1GB RAM and 128MB graphics is usually fine, higher is better. See here for tips on improving graphics performance on slower machines.

Install Java J2SE 6 or higher. Available here. It's better to download the JDK (Java Development Kit), which includes command line tools for Java. If there are any problems with the preinstalled version of Java on Linux, install a local copy in your home directory and change the PATH variable as appropriate.

From version 1.2.0 the libraries for Java3D are included with the download. There is no need to install this separately. Also, jar files and binaries for HDF5 and Jython are included with the standard release.

Install NEURON (available here) if you'll be running simulations in this environment. Note: for Mac users, you'll need to install the Developer Tools (XCode) in addition to the NEURON *.dmg. For Linux, make sure you have the packages gcc, ncurses and ncurses-devel installed. More tips on interaction with NEURON here

Install GENESIS (available here) if you'll be running simulations in this environment. More tips on interaction with GENESIS here

Installation using automatic installers

The simplest way to install neuroConstruct is to use the automatic installers for Windows, Linux and Mac (though it's best to use the manual install for Vista/Win64). Save the appropriate installer file to your hard drive and run it.

  Windows: double click on the neuroConstruct_1.x.x.exe file (where 1.x.x represents the current version number)

  Linux: change the permission of the neuroConstruct_1.x.x.sh file (chmod u+x neuroConstruct_1.x.x.sh) and run it in a terminal (./neuroConstruct_1.x.x.sh)

  Mac: install the *.dmg file in the usual way.

Select the install location. NOTE: it's best not to use a directory with a space in the name (though Program Files on Windows is fine). By default the Windows installer puts the code into C:\Program Files\neuroConstruct_1.x.x or a location of your choice, and the application can be launched via the desktop icon, or via Start -> Programs -> neuroConstruct_1.x.x. There is also a link to the documentation in this menu, or the HTML files are available at: C:\Program Files\neuroConstruct_1.x.x\docs\website\docs.

With the Linux installer you should choose an appropriate directory, e.g. /home/myuser/neuroConstruct_1.x.x. A desktop link should be automatically created, but this may vary depending on the Linux distribution. In any case there will be an executable: /home/myuser/neuroConstruct_1.x.x/neuroConstruct which can be run in a console to start the application.

Clicking on the Mac installer will extract an executable which when run puts the application in /Applications/neuroConstruct_1.x.x. A desktop link will be created but the best way to run it is to open a Terminal, go to /Applications/neuroConstruct_1.x.x and execute ./neuroConstruct.

Manual installation with zip file

If a manual install is preferred, there is a neuroConstruct zip file available for download with a directory tree from neuroConstruct_1.x.x, containing the main jar file and directories with the examples, documentation, etc. Unzip this to a convenient location e.g. to C:\neuroConstruct_1.x.x (Windows), /home/myuser/neuroConstruct_1.x.x (Linux), /Applications/neuroConstruct_1.x.x (Mac)

On Vista, the installed files under C:\Program Files\neuroConstruct_1.x.x have read/write permissions designed to make modification of installed files difficult. This has an impact on the examples which are under this directory. These problems can be solved by browsing to the folder, and recursively setting Full access control for the current user to all files in that directory via right click -> Properties -> Security -> Edit....

Building and running

To run after using automatic installer:

There should be a desktop shortcut and/or a start menu entry to launch the application.

To run manually:

Open a command prompt/shell (Windows: Start -> Programs -> Accessories -> Command Prompt and type cd C:\neuroConstruct_1.x.x, Linux: Open a terminal/console and type cd /home/myuser/neuroConstruct_1.x.x, Mac: Applications -> Utilities -> Terminal and type cd /Applications/neuroConstruct_1.x.x).

Run neuroConstruct by typing nC.bat (Windows) or ./nC.sh (Linux/Mac). NOTE: you may have to update the variable NC_HOME in this file to the correct install location of neuroConstruct!!

For Windows, you can also double click on nC.bat in the file explorer. Under Linux and Mac you might need to run chmod u+x nC.sh before you can run the file by typing ./nC.sh

The -Xmx500M used in these files (i.e. request to the JVM to have 500MB as the max Java heap size) is there to ensure enough memory for the graphics. Alter according to your machine's capabilities (approx 50% of max memory available). NOTE: it's been found that requesting too much memory for neuroConstruct under Windows can result in the application crashing when the graphics card is required to display large networks; aim for less than half the available RAM. See points on displaying large 3D networks here

The included examples should be listed under the menu item File. Run these to get a feel for the application, or follow the tutorials

More details of interacting with NEURON/GENESIS on various platforms is available here

To build from the source code (ensure you have a JDK (Java Development Kit) installed):

Type nC.bat -make (Windows) or ./nC.sh -make (Linux/Mac).

Alternatively, use Ant:

1. Install Ant (available here)
2. In the directory you have installed the code (contains build.xml) type ant

To run the application using Ant:

1. Type ant run

Type ant -p to view other options.

Post installation

Check that the location of the NEURON home dir is properly set. Go to Settings -> General Properties & Project Defaults for this. Also check on the command line for running executables in a new terminal window via Java. The suggested command lines have been tested on WinXP, Red Hat Linux and SUSE. neuroConstruct has been tested on Macs, but the interaction with NEURON/GENESIS can use some polishing. See here

When the application is run for the first time, it will create 2 files in a directory .neuroConstruct in your home directory:

Do not edit these files directly! Use Settings -> General Properties for this.