endogenous_molecular_network_attractors

Working scripts of Chu X-Y, Jiang L-H, Zhou X-H, Cui Z-J, Zhang H-Y. Evolutionary Origins of Cancer Driver Genes and Implications for Cancer Prognosis. Genes. 2017; 8(7):182., for calculating endogenous molecular network's attractors.

Basic Usage:

Before compute attrators, please confirm requirments below:

• python2.7, other 2.x may also work, python3.x are not supported because exec changed in python3.x
• scipy

- Without start input

$ python attractors.py -net ./network_origion.xlsx

 -net indicate the path of network file, attracors will be saved in ./Attractors by default.

- With start input

$ python attractors.py -net ./network_origion.xlsx --start_list_path ./Input_file.txt

--start_list_path indicate the path of initial relative activities/concentrations for all the nodes in the network.

The inputfile should be like the following format:

    1	0.0
    2	0.0
    3	0.0
    ...
    11	0.0
    12	0.0
    13	0.0

left is the nodes number, it should start from 1;   right is its value which should be float, use \t to sepreate them.

More parameters setting, type this:

$ python attractors.py -h

Results:

The attractors are something like follows:

691	['0.0000', '0.0000', '1.0000', '0.0000', '0.0000', '0.9543', '0.9306', '0.9306', '0.0000', '0.8402', '0.0000', '0.8259', '0.8184', '0.9170', '0.8694', '0.9405', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '1.0000', '0.0000', '1.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000']
128	['0.0000', '0.0000', '1.0000', '0.0000', '0.0000', '0.9543', '0.9306', '0.9306', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '1.0000', '0.0000', '1.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000', '0.0000']   

first column is the size of attractor, list is attractor.