TimeXNet can be run in three ways using the same jar file.
Single run from command line: Runs TimeXNet once using specific values for gamma1 and gamma2 parameters. The values of gamma1 and gamma2 decide the number of genes to be included in the final soluion from the initial response genes and the intermediate genes, respectively.
Single run from user interface: Launches a user intreface that prompts the user to enter all the input arguments and runs TimeXNet once for the specified gamma1 and gamma2 values.
Iterative run from command line: Runs TimeXNet iteratively for a range of gamma1 and gamma2 values to identify the best combination for the most reliable network solution.
The input parameters for all three methods of running the program are significantly similar with slight differences for the Iterative run from command line.