A translator of threshold Boolean networks into Reaction Systems

Implementation of the encoding of threshold Boolean networks into Reaction Systems proposed in:

The source code of the tool is available here:

This software tool, written in C, takes a description of a threshold Boolean network and returns the set of rules of the Reaction System simulating the network. The description of the Boolean network is given in a text file named genes.txt defined as follows. The first line of the file must contain the number of nodes of the Boolean network. The subsequent lines describe each single node of the network. Each line contains the name of the node, followed by a boolean value which specifies whether the node is self-activating, 1, or not, 0, and, finally, by the value of the related threshold. After the description of the nodes, the subsequent lines describe each single edge of the network. First of all we have a line with the number of edges. Then, we have a line describing each edge in which we have the ending node, Sj, the starting node, Si, and a value that can be either a positive or a negative integer depending on the type of influence of Si on Sj (promotion or inhibition, respectively). Several controls have been implemented in our tool in order to be sure that file genes.txt describes a consistent boolean network.

As an example, the input file corresponding to the network depicted in the figure on the right with all thresholds set to 0 should be the following. 

4
A 1 0
B 0 0
C 1 0
D 0 0
8
A C -1
A D 1
B A 1
B C -1
B D 1
C B 1
C D -1
D C 1