Boolean networks simulator
Description
This program simulates a specific family of dynamic boolean digraphs (called K* digraphs). For a given order, it generates the graph and calculates its Φ property, corresponding to the maximum of fixed points any function applied to the graph can get.
Boolean network
A boolean network is a dynamic graph with each node being associated to a transition function which, in our case, will always return a boolean value.
Each node can then be updated by applying this function with parent nodes values as parameters.
K* digraph
A K* digraph can be built in a similar way than a complete digraph (K digraph). But, it “expands” each node into several ones forming, for an order n K* digraph, n groups of n nodes.
Each of these groups is formed as a cycle containing one representing node.
To build the digraph, we represent each node by coordinates. The x value of these coordinates will always be the group the node belongs to. The y value will be its identifier within this group. The representing node of each group will then be those where the x and the y value are the same.
Each representing node is then linked to every other node for which the y value is equal to its own y (and of course also x here) value.
Here's an example with order 3 K* digraph:
For the sake of optimization and simplicity, this program generates a simpler (but equivalent) version of K* digraphs by fusing each representing node with its only parent. Here's an example still at order 3:
Fixed points
Let x a set of boolean values applied to the nodes of the graph. Given f the current transition function of the graph, x is a fixed point if f(x) = x.
In other words, x is a fixed point if the set of values of the graph is still equals to x after all its nodes has been updated.
Building the program
Run build.sh script. .class files are stored in the bin/ folder.
This script also generates the Javadoc files and stores them into doc/ folder.
Run the program
Run run.sh script.
The following command will compute the simulation with the K* graph at order x (with x an integer with minimum value of 3):
$ run.sh x
If no parameter x is given, the simulation will run with K* graph at order x.
By default, the simulation will display percentages of running progression. To disable that functionality, add the -n option after x. For example:
$ run.sh x -n
Warning: the complexity of this program is growing exponentially with the order of the K* digraph. The simulation can take a lot of time to compute even at small orders.
Bug reports
If you find any bug while running the simulation, please open an issue on the Github repository's issue tracker. Explain clearly how the bug happened and when. No special structure in the bug report is needed.
If you have any improvement suggestion, please also open an issue in the same issue tracker.
Contributing
You can modify the code by forking the repository on your account. If you then want to add your own modifications to the main repository, please open a pull request explaining your modifications.