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Author: Harald Schilly
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Compute Environment: Ubuntu 18.04 (Deprecated)

BooleaNet in the "Python 2 (Ubuntu Linux)" kernel

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# %load https://raw.githubusercontent.com/ialbert/booleannet/master/examples/tutorials/t-02.py import pylab from boolean2 import Model # # This initial condition leads to a cycle of period 4. # If A is set to False, a steady state is obtained. # # text = """ A = True B = False C = False D = True B* = A or C C* = A and not D D* = B and C """ model = Model( text=text, mode='sync') model.initialize() model.iterate( steps=15 ) # the model data attribute holds the states keyed by nodes for node in model.data: print node, model.data[node] # this is a helper function that reports the cycle lengths # and the index at wich the cycle started model.report_cycles() # # the same thing as above but # will not print only return the two parameters # print model.detect_cycles() # # this is how one plots the values, delete this below # if matplotlib is not installed # p1 = pylab.plot( model.data["B"] , 'ob-' ) p2 = pylab.plot( model.data["C"] , 'sr-' ) pylab.legend( [p1,p2], ["B","C"]) pylab.ylim((-0.1,1.1)) pylab.show()
A [True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True] C [False, False, True, True, False, False, True, True, False, False, True, True, False, False, True, True] B [False, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True] D [True, False, False, True, True, False, False, True, True, False, False, True, True, False, False, True] Cycle of length 4 starting at index 1 (1, 4)
/usr/local/lib/python2.7/dist-packages/matplotlib/legend.py:634: UserWarning: Legend does not support [<matplotlib.lines.Line2D object at 0x7f46bb75a850>] instances. A proxy artist may be used instead. See: http://matplotlib.org/users/legend_guide.html#using-proxy-artist "#using-proxy-artist".format(orig_handle) /usr/local/lib/python2.7/dist-packages/matplotlib/legend.py:634: UserWarning: Legend does not support [<matplotlib.lines.Line2D object at 0x7f46bd83be10>] instances. A proxy artist may be used instead. See: http://matplotlib.org/users/legend_guide.html#using-proxy-artist "#using-proxy-artist".format(orig_handle)
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# %load https://raw.githubusercontent.com/ialbert/booleannet/master/examples/tutorials/t-03.py import boolean2 from boolean2 import Model # # Random sampling of initial conditions # # If A is set to False, a steady state is obtained. # # text = """ A = True B = Random C = Random D = Random B* = A or C C* = A and not D D* = B and C """ seen = {} # # the key will be the fingerprint of the first state #(some random inital conditions may be the same), it is fine to overwrite in this case # as the 'sync' update rule is completely deterministic # for i in range(10): model = Model( text=text, mode='sync') model.initialize() model.iterate( steps=20 ) # detect the cycles in the states size, index = model.detect_cycles() # fingerprint of the first state key = model.first.fp() # keep only the first 10 states out of the 20 values = [ x.fp() for x in model.states[:10] ] # store the fingerprinted values for each initial state seen [ key ] = (index, size, values ) # print out the observed states for first, values in seen.items(): print 'Start: %s -> %s' % (first, values)
Start: 0 -> (4, 1, [0, 1, 2, 3, 4, 1, 2, 3, 4, 1]) Start: 1 -> (4, 0, [1, 2, 3, 4, 1, 2, 3, 4, 1, 2]) Start: 3 -> (4, 0, [3, 4, 1, 2, 3, 4, 1, 2, 3, 4]) Start: 4 -> (4, 0, [4, 1, 2, 3, 4, 1, 2, 3, 4, 1]) Start: 5 -> (4, 1, [5, 2, 3, 4, 1, 2, 3, 4, 1, 2])
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# %load https://raw.githubusercontent.com/ialbert/booleannet/master/examples/tutorials/t-05.py # # # The collector helper function # # Asynchronous updating rules are non deterministic and # need to be averaged over many runs # # The collector class makes this averaging very easy. It takes # a list of states and nodes to build a data structure that # can compute the average the state of each node over all simulation and each timestep. # # The output of averaging (in the normalized mode) is a value between # 0 and 1 representing the fraction of simulation (multiply by 100 to get percent) # that had the node in state True. # # import boolean2, pylab from boolean2 import util text = """ A = True B = Random C = Random D = Random B* = A or C C* = A and not D D* = B and C """ coll = util.Collector() for i in range(50): model = boolean2.Model( text, mode='async') model.initialize() model.iterate( steps=15 ) # # in this case we take all nodes # one could just list a few nodes such as [ 'A', 'B', 'C' ] # nodes = model.nodes # # this collects states for each run # coll.collect( states=model.states, nodes=nodes ) # # this step averages the values for each node # returns a dictionary keyed by nodes and a list of values # with the average state for in each timestep # avgs = coll.get_averages( normalize=True ) # make some shortcut to data to for easier plotting valueB = avgs["B"] valueC = avgs["C"] valueD = avgs["D"] # # plot the state of the nodes # p1 = pylab.plot( valueB , 'ob-' ) p2 = pylab.plot( valueC , 'sr-' ) p3 = pylab.plot( valueD , '^g-' ) pylab.legend( [p1,p2,p3], ["B","C","D"]) pylab.show()
/usr/local/lib/python2.7/dist-packages/matplotlib/legend.py:634: UserWarning: Legend does not support [<matplotlib.lines.Line2D object at 0x7f46bb54d590>] instances. A proxy artist may be used instead. See: http://matplotlib.org/users/legend_guide.html#using-proxy-artist "#using-proxy-artist".format(orig_handle) /usr/local/lib/python2.7/dist-packages/matplotlib/legend.py:634: UserWarning: Legend does not support [<matplotlib.lines.Line2D object at 0x7f46bb5ead10>] instances. A proxy artist may be used instead. See: http://matplotlib.org/users/legend_guide.html#using-proxy-artist "#using-proxy-artist".format(orig_handle) /usr/local/lib/python2.7/dist-packages/matplotlib/legend.py:634: UserWarning: Legend does not support [<matplotlib.lines.Line2D object at 0x7f46bb54dd90>] instances. A proxy artist may be used instead. See: http://matplotlib.org/users/legend_guide.html#using-proxy-artist "#using-proxy-artist".format(orig_handle)
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