Aging of Evolving Genomes In Silico (AY-jis, /eɪd͡ʒɪs/)
Numerical model for life history evolution of age-structured populations under customizable ecological scenarios.
We recommend that you install aegis-sim
from PyPI into a virtual environment.
$ pip install aegis-sim
If you will using the jupyter notebook visualization script, you might need to run jupyter nbextension enable --py widgetsnbextension
to activate widgets.
Cheat sheet
# Unix/macOS
python3 -m venv aegis-venv
. aegis-venv/bin/activate
python3 -m pip install aegis-sim
# Windows
python -m venv aegis-venv
.\aegis-venv\Scripts\activate
python -m pip install aegis-sim
For developers
# Unix/macOS
git clone git@github.com:valenzano-lab/aegis.git
cd aegis
make install_dev
To check if installation is successful, run aegis -h
. If it is, the output will contain Aging of Evolving Genomes In Silico
; if not, it will say aegis: command not found
.
-
Create a configuration file
Before running a custom AEGIS simulation, you must create a configuration file (in YAML format) which will contain your custom parameter values. List of modifiable parameters, and all relevant details can be found in the wiki. Default parameter values are set in the file default.yml.
An example of a YAML file:
# custom.yml RANDOM_SEED: 42 STAGES_PER_SIMULATION: 10000 AGE_LIMIT: 50
-
Start the simulation
$ aegis {path/to/file}.yml # In this case, `aegis custom.yml`