mushthofa / ASPG

ASP-based attractor computation

ASPG

ASP-based attractor computation

PREREQUISITES:

1. Install Python 3 on your system
2. Download and compile the latest version of iclingo solver at:

http://sourceforge.net/projects/potassco/files/iclingo/

and make sure that it is placed in the binary path of the system, i.e., you can call the program using:

(A source distribution is also included)

$ iclingo -v iclingo 3.0.5 (clasp 1.3.10) ....

HOW TO USE:

1. Write a file to describe the network structure in ASP format. Each node is declared using the ASP fact: protein(X). while each activation/inhibition between two nodes is declared using the ASP fact: activates(X, Y). or inhibits(X, Y).

For example:

% Proteins a,b and c where a activates b and c inhibits a
protein(a).
protein(b).
protein(c).

activates(a,b).
inhibits(c,a).

2. Call the attractor computation program using the syntax:

   $ python3 attractor.py filename size [0|1] [a|s]

where filename is the file containing the network description, 0=activation rule r*, 1=activation rule r+, a=asynchronous update, s=synchronous update. For example, if the network description above is stored in file 'network.txt', then to compute the attractors of the network when using activation rule r* and synchronous update, run the following command:

$ python3 attractor.py network.txt 3 0 s

Some example network description files: 'toy-3nodes.txt', 'toy-4nodes.txt', 'yeast.txt' and 'th.txt' are provided.