seeds 1.0.2

Stochastic Ecological and Evolutionary Dynamics System

Created by:

Brian Connelly <[e-mail]> and Luis Zaman <[e-mail]>

Website:

https://github.com/briandconnelly/seeds

Expanded Documentation:

The primary source for documentation is the SEEDS website. Here, detailed installation instructions, how-to guides, code templates, and example experiments are provided.

Installing SEEDS:

SEEDS requires the NetworkX package, available at http://networkx.lanl.gov/. Additionally, SEEDS requires Python version 2.6.5 or greater.

SEEDS can be installed using the included setup.py script by running “python setup.py install”.

If you specified the directory into which SEEDS was installed, you will need to make sure it is searchable in your Python environment. This can be done by placing the directory into which it was installed in your PYTHONPATH.

Running SEEDS:

Out of the box, SEEDS includes simple experiments in the examples directory. These experiments can be run once SEEDS has been installed on your system. See the README.txt file in a specific directory to learn about the experiment, how to configure it, and how to perform it.

Expanding SEEDS:

SEEDS is designed as a plugin-based framework. This means that you can create and use your own cell types, topologies, and actions and use these immediately without modifying the base SEEDS framework.

To create experiments that model behaviors of interest to you, a Cell type will need to be created. More information on this process can be found on the SEEDS website. Additionally, sample Cell types can be found in the examples directory.

Once you have created your additional types or actions, place them in a directory called “plugins”, and edit seeds.cfg, instructing the experiment to use them. For cell types, change the value of the “cell” parameter in the “Experiment” section. For topologies, change the value of the “topology” parameter in the “Experiment” section. For actions, add it to the comma-separated “actions” parameter in the “Experiment” section. Parameters to your plugins can be set in the seeds.cfg file in the section you define in your code.

License:

Seeds is released under the Apache License, Version 2.0. For more information, see the files LICENSE.txt and NOTICE.txt.