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Installation

The Java Platform, Standard Edition Runtime Environment (JRE) 1.7 or higher is required to be installed (Java SE is available at here). have tested NetLand under 64-bit version of Windows 7 and Windows 10, Linux Fedora 18 and Mac OS X 10.8 Mountain Lion.

The current NetLand package includes the following files.

  • Two shell scripts, "runNetLand.bat" and "runNetLand.sh", for launching NetLand in different operating systems.
  • A jar file “main.jar”. It should be in the same directory as shell scripts.
  • Two folders namely "toy models" and "saved results" which contain toy gene network files and pre-computed results respectively.
  • A folder namely "lib". It contains the required libraries to launch NetLand.
  • A folder namely "GPDM" which contains the executable files required for running "GPDM" program in NetLand. Make sure you have the execute permissions to the executable files. To check the permission of a file, the command is "ls -l filename". Use "chmod 705 filename" to obtain the execute permission.

    • Note that the scripts must be in the same directory as the “GPDM” folder and "lib" folder.

    To run the "GPDM" program, DLL (Dynamic Link Library) of BLAS, LAPACK and GFORTRAN are required. The DLL files for Windows OS are in the GPDM/win folder. For Mac OS, please check if libblas.dylib, liblapack.dylib and libgfortran.dylib are under /usr/lib/. Otherwise users should install the libraries themselves.

    The BLAS, LAPACK and GFORTRAN can be downloaded from

  • LAPACK, see http://www.netlib.org/lapack/
  • BLAS, see http://www.netlib.org/blas/
  • GFORTRAN, see https://gcc.gnu.org/wiki/GFortranBinaries#MacOS

    • Then follow the installation instructions in the package. For Linux, users can use the command, e.g. yum, to install these packages.

    To launch NetLand

  • Under Windows, double click the “runNetLand.bat”.
  • Under Linux, run the command “./runNetLand.sh” in a terminal.
  • Under Mac OS X, run the command “./runNetLand.sh” in a konsole.

    • Make sure you have the execute permissions to the scripts. To check the permission, the command is “ls –l filename”. Use “chmod 705 filename” to gain the executive permission. For Windows users, please check if "java" is in your system path. If not, you can either add it to the system path or add the full path of "java.exe" to the script.

    Example: "C:\Program Files\Java\jre1.8.0_31\bin\java.exe" -classpath "lib\*;main.jar" WindowGUI.NetLand


    The detailed instructions can be found from the user manual.