Araudia ======= .. image:: images/index.png :align: right :width: 400 :alt: Araudia model and example simulation output **Araudia** is a stochastic simulation platform to study the origins of regulation and agency in evolving (proto)cell ecologies. Specifically, the platform implements a microbial consumer-resource model with the following extensions: - The chemostat containing the microbial ecology can have **time-dependent nutrient sources** applied. - **Evolutionary operators** are implemented so that organisms can adapt over time (via minor mutations or more major innovations). - Organisms can possess an **internal regulatory network** (implemented as a neural ODE) which can evolve to dynamically change the nutrient preference of the organism over short time scales, dependent on prevailing internal and external conditions. Thus, organisms can learn better short-term survival strategies. - The simulation runs with **stochastic dynamics**. **Araudia** was originally developed for :ref:`Our Paper` concerned with the origins of regulatory mechanisms in prebiotic protocells at the origins of life. However, the platform can be also used in a wider context -- for example, it can be used as a standard microbial consumer-resource model with/without evolution. See the Supplementary Information of :ref:`Our Paper` for a full technical description of the model. The software is written in Python and is available as an `open source repository on Bitbucket `_ under a `GPL v3 License `_. The current version is v1.0. .. image:: images/screenshot.png :align: right :width: 400 :alt: Araudia command line screenshot To get a sense of the capabilities of the platform, follow the :ref:`Installation` instructions and try some of the :ref:`Illustrative Demos`. ---------------- šŸ’” Developed in Donostia-San SebastiĆ”n, Spain, "Araudia" is a Basque word translated as a 'set of rules/regulations' or 'code of conduct'. The platform investigates under what conditions protocells can evolve appropriate codes of conduct to dynamically deal with environmental changes over short time scales. ---------------- .. toctree:: :maxdepth: 2 :caption: Contents: installation demos simulation analysis issues architecture cite