seeds 1.0.7

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 Wiki. Here, detailed installation instructions, how-to guides, code templates, and example experiments are provided.

Installing SEEDS:

SEEDS requires Python version 2.6.5 or greater. Additionally, SEEDS requires the NetworkX package.

Installation is done using the standard Python Distribution Utilities and can be as straightforward as running “python setup.py install”. For further instructions on this process, please see the SEEDS Wiki or the official Distutils documentation at http://docs.python.org/install/index.html.

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.

Reporting Bugs and Feature Requests:

SEEDS is under constant development. To see which features and changes are planned or to report bugs, visit http://github.com/briandconnelly/seeds/issues.

License:

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