Aging of Evolving Genomes In Silico (AY-jis, /eɪd͡ʒɪs/)
Numerical model for life history evolution of age-structured populations under customizable ecological scenarios.
You can run AEGIS simulations on a webserver or locally. The webserver is especially useful if you want to try AEGIS out and run a couple of simple simulations. For more demanding simulations, it is best to install and run AEGIS on your local machine.
You can access the AEGIS webserver here. The server is running AEGIS GUI.
You can install AEGIS locally using pip (pip install aegis-sim). The package is available on https://pypi.org/project/aegis-sim/. You can use AEGIS with a GUI or in a terminal. GUI is useful for running individual simulations, while the terminal is useful for running batches of simulations.
python3 -m aegis # starts GUI
python3 -m aegis -c {path/to/config_file} # runs a simulation within a terminal
python3 -m aegis --help # shows help documentationTo run simulations within a terminal, you need to prepare config files in YAML format which contain custom values for simulation parameters. The list of parameters, including their descriptions and default values you can find here. An example of a config file:
RANDOM_SEED: 42
STEPS_PER_SIMULATION: 10000
AGE_LIMIT: 50If you want to contribute to the codebase, install AEGIS from github:
git clone [email protected]:valenzano-lab/aegis.git
cd aegis
make install_devMost documentation about the model is available within the GUI itself, including description of submodels, configuration parameters, output specification, and genetic architecture. Use the webserver or a local installation to access the GUI. Further information is available in scientific articles:
- AEGIS: An In Silico Tool to model Genome Evolution in Age-Structured Populations (2019)
- An In Silico Model to Simulate the Evolution of Biological Aging (2016)
Exhaustive, searchable API reference made by pdoc is available here.