This is a package we developed for the DREAM3 in silico gene regulatory network reconstruction competition (Yip et al., PLoS ONE 5(1):e8121, 2010). To run the program, Java and Apache Ant need to be installed. Then unzip all the files into a directory, and use a command window to type "ant runall3" at the directory to run the program. In order to keep the package size small, we have only included the DREAM3 size-10 networks. The size-50 and size-100 networks can be downloaded from the DREAM3 web site.
The program was developed mainly for DREAM3, and was not written in a very generic way. To run it on other datasets or to use to for some other tasks, the source code needs to be modified.