Symbulation – Agent based modeling of symbiont ecology and evolution¶
Anya Vostinar and contributors.
Symbulation is an artificial life software tool for agent-based modeling of the evolution of biological symbiosis, which can occur along the spectrum between parasitism and mutualism.
Interested in starting a new project with Symbulation? We have a cookiecutter template here: https://github.com/anyaevostinar/SymbulationProjectTemplate.
Symbulation is built with the Empirical platform and the cookiecutter includes our recommended directory layout and example analysis files.
Install the latest Cookiecutter:
pip install -U cookiecutter
Generate an Symbulation project:
Move into the new project directory and the
SymbulationEmp directory and make:
cd SymbulationProject/SymbulationEmp make
Make any changes that you wish to the file
SymSettings.cfg and then run:
By default, your data will be output to the files
We recommend that you copy your
symbulation executable to your
cp symbulation_default ../Data/sample_treatment cd ../Data/sample_treatment
You can then use the provided Python script to run several replicates:
You can also then use the provided Python script to transform your data into a format more easily used by R:
cd ../../Analysis/sample_treatment python3 munge_data.py
And then open our provided R script
SampleAnalysis.R in R, set your working directory to the
Analysis directory and then run all lines to observe the effect of vertical transmission rate on the interaction value evolved.
Created part of my free logo at LogoMakr.com.
This is a software model of symbiosis which allows for evolution of parasitism and mutualism.
Click here to try it out in your web browser!
Checkout our quick start guides for more information on getting started.
Search for any function, class or variable using the search feature in the top left!
Table of Contents¶
- Getting started with Symbulation development
- Coding guidelines and review checklist
- Documentation for Symbulation Documentation
- Guide to Testing in Symbulation