GNC: Gene Network Coherence with direct and indirect relationships
This is a Java-based software tool for analyzing gene networks coherence using direct and indirect relationships. This tool can be used in linux, mac, and windows plataforms. In addition, GNC software is parallelized using a multi-threading design.
To use the application, please, download the GNC.zip file. Inside this zip file, there is a folder called "GNC". This folder contains several crucial information of the executable file. Also, it contains some gene networks for testing the tool grouped as "Input Network" and "Biological Databases".
Moreover, the source code of the command client is also provided.
Usage information
To launch the app, extract the zip file. There are available two different implementations; a java swing GUI interface and a command line program. If you have any question about the use of the software, please read "User Guide.pdf" file.
Troubleshooting and F.A.Q.
- Be patient. Although this program is optimized, usually it takes a long time, specially if you use files bigger than 1 MB.
- Make sure that you have the JVM 1.5 or later.
- Give to Java Virtual Machine enough memory. At least 2048 MB. The more memory you provide to the app, the better performance you get.
- News input network and biological databases files must be a “.txt” file and it must have the following format:
Node1,Node2
Node1,Node3
...
Node1,Node N
...
Node N, Node M
- Please, do not modify or handle the "GNC" folder.
- For further information see the "User Guide.pdf" file provided.
COPYRIGHT
Francisco Gómez Vela (fgomez@upo.es), José Antonio Lagares (jalagrod@gmail.com) and Norberto Díaz-Díaz (ndiaz@upo.es).
Copyright © 2014 Universidad Pablo de Olavide, Spain.