Network Classes

Neet provides a collect of pre-defined network types which are common models of complex systems, including

boolean.ECA	ECA represents an elementary cellular automaton rule.
boolean.RewiredECA	RewiredECA represents elementary cellular automaton rule with a rewired topology.
boolean.WTNetwork	WTNetwork represents weight-threshold boolean network.
boolean.LogicNetwork	LogicNetwork represents a network of logic functions.

These concrete network types are leaves in a hierarchy:

All networks in Neet ultimately derive from the Network class which provides a uniform interface for all network models. This class provides a basic interface in and of itself, but derives from StateSpace and LandscapeMixin to provide a wealth of additional features. See State Spaces and Attractor Landscapes for more information.

Basic Network Attributes

As an example, consider the boolean network boolean.examples.s_pombe, which is a gene regulatory network model of the cell cycle of S. pombe (fission yeast) [Davidich2008]. All networks have a “shape”, namely an array of the number of states each node can take — it’s base.

>>> s_pombe.shape
[2, 2, 2, 2, 2, 2, 2, 2, 2]

Along with this, comes the ability to ask how many nodes the network has:

>>> s_pombe.size
9

In general, Neet’s networks need not be uniform; each state can have a different base. However, all of the networks currently implemented are Boolean, meaning that every node in the network has a binary.

In addition to specifying the base of the nodes of the network, each node can be given a name.

>>> s_pombe.names
['SK', 'Cdc2_Cdc13', 'Ste9', 'Rum1', 'Slp1', 'Cdc2_Cdc13_active', 'Wee1_Mik1', 'Cdc25', 'PP']

Further, on the whole you can associate an arbitrary dictionary of metadata data, for example citation information.

>>> s_pombe.metadata['citation']
'M. I. Davidich and S. Bornholdt, "Boolean network model predicts cell cycle sequence of fission yeast," PLoS One, vol. 3, no. 2, p. e1672, Feb. 2008.doi:10.1371/journal.pone.0001672'

Dynamic State Update

Beyond data such as these, concrete classes specify information necessary for describing the dynamics of the network’s state. Unlike most dynamical network packages, Neet’s networks do not store the state of the network internally. Instead, the API provides methods for operating on state external to the network. In particular, Network.update() which updates a state of the list or numpy.ndarray in place.

>>> state = [0, 1, 1, 0, 1, 0, 0, 1, 0]
>>> s_pombe.update(state)
[0, 0, 0, 0, 0, 0, 0, 1, 1]
>>> state
[0, 0, 0, 0, 0, 0, 0, 1, 1]

This single function allows Neet to implement a number of common analyses such as landscape, information and sensitivity analyses.

Graph Structure

As dynamical networks, all Network instances have a directed graph structure. Neet provides a minimal interface for exploring this structure. At it’s basic, you can probe which nodes are connected by an edge:

# source nodes of edges incoming to node 6
>>> s_pombe.neighbors(6, direction='in') == {1, 6, 8}
True

# target nodes of edges outgoing from 6
>>> s_pombe.neighbors(6, direction='out') == {5, 6}
True

# all nodes connected to node 6
>>> s_pombe.neighbors(6, direction='both') == {1, 5, 6, 8}
True

# all nodes connected to node 6
>>> s_pombe.neighbors(6, direction='both') == {1, 5, 6, 8}
True

Of course, this will only get you so far. Luckily, the NetworkX package provides a whole host of graph-theoretic analyses. To take advantage of that fact, and not avoid Neet reinventing the wheel, you can export your Neet network as a networkx.DiGraph.

>>> import networkx as nx
>>> g = s_pombe.network_graph()
>>> nx.shortest_path(g, 1, 5)
[1, 2, 5]
>>> g = s_pombe.network_graph(labels='names')  # default labels='indices'
>>> nx.shortest_path(g, 'Cdc2_Cdc13', 'Cdc2_Cdc13_active')
['Cdc2_Cdc13', 'Ste9', 'Cdc2_Cdc13_active']

You can draw the graphs, with the nodes labeled by either the node index

>>> s_pombe.draw_network_graph({'labels': 'indices'}, {
...    'path': 'source/static/s_pombe_indices.png',
...    'display_image': False
... })

or labeled by the node name:

>>> s_pombe.draw_network_graph({'labels': 'names'}, {
...    'path': 'source/static/s_pombe_names.png',
...    'display_image': False
... })

Note

For the drawing functionality, you will need to install the optional dependencies: Graphviz and pygraphviz. See Getting Started.