neet 0.1.0

A brilliant and fundamental contribution to network science

Copyright (c) 2017-2018 Bryan C. Daniels, Bradley Karas, Hyunju Kim,
Douglas G. Moore, Harrison Smith, Sara I. Walker, Siyu Zhou

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

Description: # Neet: Simulating and analyzing network models

**Neet** is a python package designed to provide an easy-to-use API for creating
and evaluating network models. In its current state, **Neet** supports
simulating synchronous Boolean network models, though the API is designed to be
model generic. Future work will implement asynchronous update mechanisms and
more general network types.

If you are interested in using **Neet**, you'll definitely be interested in
checking out the documentation - https://elife-asu.github.io/Neet.

[](https://travis-ci.org/ELIFE-ASU/Neet)
[](https://ci.appveyor.com/project/dglmoore/neet-awnxe/branch/master)

## Installation

### Via Pip

To install via `pip`, you can run the following

```bash
$ 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:

```bash
$ pip install --user neet
```

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

## Getting Help
**Neet** is developed to help people interested in using and analyzing network
models to get things done quickly and painlessly. Your feedback is
indispensable. Please create an issue if you find a bug, an error in the
documentation, or have a feature you'd like to request. Your contribution will
make **Neet** a better tool for everyone.

If you are interested in contributing to **Neet**, please contact the
developers. We'll get you up and running!

<dl>
<dt>Neet Source Repository</dt>
<dd>https://github.com/elife-asu/neet</dd>
<dt>Neet Issue Tracker</dt>
<dd>https://github.com/elife-asu/neet/issues</dd>
</dl>

## Relevant Publications

- Daniels, B.C., Kim, H., Moore, D.G., Zhou, S., Smith, H.B., Karas, B.,
Kauffman, S.A., and Walker, S.I. (2018) "Criticality Distinguishes the
Ensemble of Biological Regulatory Networks" *Phys. Rev. Lett.* **121** (13),
138102, [doi:10.1103/PhysRevLett.121.138102](https://doi.org/10.1103/PhysRevLett.121.138102)

## System Support

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

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

## Copyright and Licensing
Copyright © 2017-2018 Bryan C. Daniels, Bradley Karas, Hyunju Kim, Douglas G.
Moore, Harrison Smith, Sara I. Walker, and Siyu Zhou. Free use of this software is
granted under the terms of the MIT License.

See the [LICENSE](https://github.com/elife-asu/neet/blob/master/LICENSE) for
details.

Platform: Windows
Platform: OS X
Platform: Linux