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.

Try out our browser-based GUI. See our documentation at https://symbulation.readthedocs.io.

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.

Usage

Install the latest Cookiecutter:

pip install -U cookiecutter

Generate an Symbulation project:

cookiecutter https://github.com/anyaevostinar/SymbulationProjectTemplate.git

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:

./symbulation_default

By default, your data will be output to the files HostVals_data__SEED10.data and SymVals_data__SEED10.data.

We recommend that you copy your symbulation executable to your Data folders:

cp symbulation_default ../Data/sample_treatment
cd ../Data/sample_treatment

You can then use the provided Python script to run several replicates:

python3 simple_repeat.py

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.

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