COMMANDS:

After downloading the file, you may need to change the file access permission to make it executable:

chmod +x boolenet

To run BooleNet in Linux or Windows Cygwin, use the command:

./boolenet input_file

For example, if you use the Boolean network model of Arabidopsis thaliana as an input file, you will get the following output:

./boolenet arabidopsis.net 101100110111011 Attractor 1 is of length 1 110110110011011 Attractor 2 is of length 1 100110110011011 Attractor 3 is of length 1 111100110111011 Attractor 4 is of length 1 010001000011100 Attractor 5 is of length 1 010001001011100 Attractor 6 is of length 1 001100110111011 Attractor 7 is of length 1 000110110011001 Attractor 8 is of length 1 000001000011100 Attractor 9 is of length 1 000001001011100 Attractor 10 is of length 1 The number of attractors is 10

INPUT FORMAT:

The input file starts with the statement:

.v number_of_vertices

which specifies the total number of vertices in the Boolean network. We assume that vertices are labeled from 1 to number_of_vertices.

Then, the description of Boolean functions associated to vertices follows in the following format:

.n vertex's_label number_of_regulators list_of_labels_of_regulators input_values output_value ... input_values output_value

For example, the description of a vertex labeled by 1 with two regulators labeled by 2 and 3, which has an associated function OR can be given as follows:

.n 1 2 2 3 00 0 01 1 10 1 11 1

It is sufficient to enumerate the input assignments for which the function evaluates to 1, i.e. the above description can be reduced to:

.n 1 2 2 3 01 1 10 1 11 1

To further reduce the description, one can use the symbol "-" meaning "both 0 and 1". Then, the above description becomes:

.n 1 2 2 3 -1 1 1- 1

A line which starts with "#" is commented out. Comments are useful for relating labels of vertices to the actual names of genes.

As an example, see the input description of the Boolean network model of Arabidopsis thaliana.