https://github.com/valenzano-lab/aegis
Numerical model for life history evolution of age-structured populations
https://github.com/valenzano-lab/aegis
aging evolutionary-biology simulation
Last synced: 3 months ago
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Numerical model for life history evolution of age-structured populations
- Host: GitHub
- URL: https://github.com/valenzano-lab/aegis
- Owner: valenzano-lab
- License: mit
- Created: 2019-05-01T22:49:54.000Z (about 7 years ago)
- Default Branch: v2
- Last Pushed: 2026-03-14T07:25:57.000Z (3 months ago)
- Last Synced: 2026-03-14T17:55:35.256Z (3 months ago)
- Topics: aging, evolutionary-biology, simulation
- Language: Python
- Homepage:
- Size: 50.1 MB
- Stars: 4
- Watchers: 3
- Forks: 2
- Open Issues: 7
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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# AEGIS
> Aging of Evolving Genomes In Silico (AY-jis, /eɪd͡ʒɪs/)
Numerical model for life history evolution of age-structured populations under customizable ecological scenarios.
## How to use
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.
### Webserver use
You can access the AEGIS webserver [here](https://genome.leibniz-fli.de/aegis/). The server is running AEGIS GUI.
### Local use
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.
```bash
aegis gui # starts GUI
aegis sim -c {path/to/config_file} # runs a simulation within a terminal
aegis --help # shows help documentation
```
To run simulations within a terminal, you need to prepare config files in [YAML](https://en.wikipedia.org/wiki/YAML) format
which contain custom values for simulation parameters. The list of parameters, including their descriptions and default values you can find [here](src/aegis/documentation/dynamic/default_parameters.md).
An example of a config file:
```yml
RANDOM_SEED: 42
STEPS_PER_SIMULATION: 10000
AGE_LIMIT: 50
```
### Developer installation
If you want to contribute to the codebase, install AEGIS from github:
```bash
python3 -m pip install -e git+https://github.com/valenzano-lab/aegis.git#egg=aegis-sim
```
If you are having installation issues, check that pip is up to date (`python3 -m pip install --upgrade pip`).
### AEGIS GUI
Graphical user interface for AEGIS can be used on the webserver or with a local installation. It contains sections for launching and analyzing/plotting simulations.
## Documentation
### Model description
Most documentation about the model is available within the GUI itself, including description of [inputs](src/aegis/documentation/dynamic/default_parameters.md), [outputs](src/aegis/documentation/dynamic/output_specifications.md), [submodels](src/aegis/documentation/dynamic/submodel_specifications.md) and the [genetic architecture](src/aegis_sim/submodels/genetics/doc.md). Use the [webserver](https://genome.leibniz-fli.de/aegis/) or a local installation to access the GUI. Further information is available in the following articles:
- [AEGIS: An In Silico Tool to model Genome Evolution in Age-Structured Populations (2019)](https://www.biorxiv.org/content/10.1101/646877v1)
- [An In Silico Model to Simulate the Evolution of Biological Aging (2016)](https://www.biorxiv.org/content/10.1101/037952v1)
Dynamically generated API reference made by pdoc is available [here](https://valenzano-lab.github.io/aegis/).
## Contributors
- **Martin Bagić** (v2): [email](martin.bagic@outlook.com), [github](https://github.com/martinbagic)
- **Dario Valenzano** (v1, v2): [github](https://github.com/dvalenzano)
- **Erik Boelen Theile** (v2)
- **Arian Šajina** (v1): [github](https://github.com/ariansajina)
- **William Bradshaw** (v1): [github](https://github.com/willbradshaw)