IntroductionExamplesModelsDocumentationDownloadLinksContact
 

Interacting with native simulators on various platforms

Outlined here are some points regarding how neuroConstruct deals with the native simulators on various operating systems

General points

neuroConstruct is written in Java and so can be used on any platform with a Java Virtual Machine together with an implementation of Java3D.

In general, NEURON and/or GENESIS should be present on the same machine as neuroConstruct. The scripts for the target platform are generated based on the network created by neuroConstruct, and these are set running in separate processes via the Java Runtime.exec() command.

Linux

  NEURON

NEURON hoc and mod files are generated from the network model in neuroConstruct. First, the mod files are compiled using nrnivmodl. This executable is found using the value for the NEURON home directory in Settings -> General Properties.

Once the native machine libraries for the channels are generated, the main hoc file is run with nrngui. Note that this is executed in a console window (by prefixing the command with gnome-terminal -x (Gnome desktop) or konsole (KDE), also set via Settings -> General Properties)

  GENESIS

GENESIS script is generated from the network model and the main file can be run straight away. The genesis command, together with the name of the main file are executed via Runtime.exec(), therefore the location of this executable should be in the PATH variable. The command is executed in a new console window as above.

Windows

  NEURON

NEURON hoc and mod files are generated from the network model in neuroConstruct. First, the mod files are compiled using a command of the form C:\nrn60\bin\rxvt.exe -e C:\nrn60\bin\sh C:\nrn60\lib\mknrndll.sh C:\nrn60. The C:\nrn60 is found using the value for the NEURON home directory in Settings -> General Properties.

Once the native machine libraries for the channels are generated, the main hoc file is run with neuron.exe.

  GENESIS

GENESIS was for many years not available on Windows. A port has recently been created, which while slower than under Linux, can be used to test generated GENESIS code under Windows. The following assumes Cygwin has been installed at C:\cygwin and GENESIS installed at /usr/local/genesis i.e. C:\cygwin\usr\local\genesis.

GENESIS script is generated from the network model and the main file can be run straight away without further compilation. The file {NEUROCONSTRUCT_HOME}/templates/genesisUtils/startxwin2.bat is used to launch the genesis executable. This is a slightly modified version of the startxwin.bat supplied with Cygwin for running an XTerm. This mechanism is a bit flaky (e.g. it doesn't like NEURON running under Cygwin at the same time). Please report any problems/solutions to bugs - at - neuroConstruct.org

Mac

neuroConstruct and its 3D visualisation capability has been successfully tested on the Mac, but the interaction with simulation platforms needs more testing. NEURON interaction is fine if the Developer Tools (XCode) are installed. Basic GENESIS interaction has been tried successfully too.

If you are interested in helping test the application on this platform, please get in touch