FAQ

1. What is the minimum RAM size needed to run NetLand?

NetLand runs on JVM (Java virtual machine) using the default settings of memories. To manually change the RAM, users can add the command line arguments "-Xmsm –Xmxm" to the shell scripts (“runNetLand.sh” and “runNetLand.bat”) using text editors. “-Xms” stands for the minimum heap size, and “-Xmx” denotes the maximum heap size.
For example, the following command allows a minimum of 2GB and a maximum of 4GB of memories used by the JVM:
java -Xms2048m -Xmx4096m -classpath "lib\*;main.jar " WindowGUI.NetLand
The memory requirement depends on the size of network model and values of parameters, e.g. the number of iterations in a simulation. A minimum memory of 20MB is required to launch NetLand. The details of memory consumption can be found in Chapter 7 of the user manual.

2. Why can't I launch NetLand by double clicking the shell script?

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
For OSX and Linux users, the script should be run under a terminal or konsole using the command "bash runNetLand.sh" or "./runNetLand.sh".

3. NetLand can't load or simulate my SBML file.

The current version of NetLand is limited to analyze models with fixed parameters and variables. It cannot simulate models with parameters and variables changing with time.
If you have trouble loading your SBML file, please contact the author Jie Zheng.

4. A message "Cannot find a steady state" shows up when I try to construct a landscape.

NetLand cannot construct the landscape of a system without a stable state. The steady state is a situation in which all state variables are constant in spite of ongoing processes that strive to change them. For example, a system with its variables exponentially increasing can never reach a steady state. And the current version of NetLand cannot construct the landscape of a system with stable oscillations.

Contact

The authors have carried out extensive testing and debugging of the program, which should be generally stable and functional if the instructions in the manual are followed. It is our hope that, with the GUI, users without much computational sophistication can also apply our algorithm to analyze their network smoothly.

However, since the authors are not professional programmers, NetLand does not behave or look like a commercial software. Please send your suggestions, comments, reports of bugs and errors to Jie Zheng. Thank you!