Introduction

Neet is a library for simulating and analyzing dynamical network models. It is written entirely in Python, with minimal external dependencies. It provides a heirarchy of network classes and facilities for analyzing the attractor landscapes, informational structure and sensitivity of those network models.

Examples

Neet provides a network classes with methods designed to make common tasks as painless as possible. For example, you can read in a collection of boolean logic equations and immediately probe the dynamics of the network, and compute values such as the LandscapeMixin.attractors and the boolean.SensitivityMixin.average_sensitivity() of the network

>>> from neet.boolean import LogicNetwork
>>> from neet.boolean.examples import MYELOID_LOGIC_EXPRESSIONS
>>> net = LogicNetwork.read_logic(MYELOID_LOGIC_EXPRESSIONS)
>>> net.names
['GATA-2', 'GATA-1', 'FOG-1', 'EKLF', 'Fli-1', 'SCL', 'C/EBPa', 'PU.1', 'cJun', 'EgrNab', 'Gfi-1']
>>> net.attractors
array([array([0]), array([62, 38]), array([46]), array([54]),
       array([1216]), array([1116, 1218]), array([896]), array([960])],
      dtype=object)
>>> net.average_sensitivity()
1.0227272727272727
>>> net.network_graph()
<networkx.classes.digraph.DiGraph object at 0x...>

See the examples directory of the GitHub repository for Jupyter notebooks which demonstrate some of the Neet’s features.

Getting Started

Installation

Dependencies

Neet depends on several packages which will be installed by default when Neet is installed via pip:

• six
• numpy
• networkx
• pyinform
• deprecated

However, network visualization is notoriously problematic, and so we have two optional dependencies which are only required if you wish to visualize networks using Neet’s builtin capabilities:

• Graphviz
• pygraphviz

True to form, these dependencies are a pain. Graphviz, unfortunately, cannot be installed via pip (see: https://graphviz.gitlab.io/download/ for installation instructions). Once Graphviz has been installed, you can install pygraphviz via pip.

Via Pip

To install via pip, you can run the following

$ pip install neet

Note that on some systems this will require administrative privileges. If you don’t have admin privileges or would prefer to install Neet for your user only, you do so via the --user flag:

$ pip install --user neet

From Source

$ git clone https://github.com/elife-asu/neet
$ cd neet
$ python setup.py test
$ pip install .

System Support

So far the python wrapper has been tested under python2.7, python3.4 and python3.5, and on the following platforms:

Note

We will continue supporting Python 2.7 until January 1, 2020 when PEP 373 states that official support for Python 2.7 will end.

• Debian 8
• Mac OS X 10.11 (El Capitan)
• Windows 10