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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.
<!-- TODO describe what aegis is for and whom is it for -->
## 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](). The server is running AEGIS GUI.<!-- TODO update link -->
### 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
```
<!-- or
```bash
git clone git@github.com:valenzano-lab/aegis.git
cd aegis
make install_dev
``` -->
If you are having installation issues, check that pip is up to date (`python3 -m pip install --upgrade pip`).
<!-- TODO update install_dev script -->
### 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.
<img width="418" alt="Screenshot_21" src="https://github.com/user-attachments/assets/520bb69c-a1cd-404a-bdf8-a541340e699a" style="border-radius: 10px;">
## 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]() or a local installation to access the GUI. <!-- TODO update link --> 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)
<!-- TODO including ODD as modeled by https://www.jasss.org/23/2/7.html-->
### API reference
Exhaustive, searchable 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)
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"description": "[](https://badge.fury.io/py/aegis-sim)\n[](https://www.python.org/downloads/release/python-360/)\n\n# AEGIS\n\n> Aging of Evolving Genomes In Silico (AY-jis, /e\u026ad\u0361\u0292\u026as/)\n\nNumerical model for life history evolution of age-structured populations under customizable ecological scenarios.\n\n<!-- TODO describe what aegis is for and whom is it for -->\n\n## How to use\n\nYou 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.\n\n### Webserver use\n\nYou can access the AEGIS webserver [here](). The server is running AEGIS GUI.<!-- TODO update link -->\n\n### Local use\n\nYou 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.\n\n```bash\naegis gui # starts GUI\naegis sim -c {path/to/config_file} # runs a simulation within a terminal\naegis --help # shows help documentation\n```\n\nTo run simulations within a terminal, you need to prepare config files in [YAML](https://en.wikipedia.org/wiki/YAML) format\nwhich 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).\nAn example of a config file:\n\n```yml\nRANDOM_SEED: 42\nSTEPS_PER_SIMULATION: 10000\nAGE_LIMIT: 50\n```\n\n### Developer installation\n\nIf you want to contribute to the codebase, install AEGIS from github:\n\n```bash\npython3 -m pip install -e git+https://github.com/valenzano-lab/aegis.git#egg=aegis-sim\n```\n\n<!-- or\n```bash\ngit clone git@github.com:valenzano-lab/aegis.git\ncd aegis\nmake install_dev\n``` -->\n\nIf you are having installation issues, check that pip is up to date (`python3 -m pip install --upgrade pip`).\n\n<!-- TODO update install_dev script -->\n\n### AEGIS GUI\nGraphical user interface for AEGIS can be used on the webserver or with a local installation. It contains sections for launching and analyzing/plotting simulations.\n\n<img width=\"418\" alt=\"Screenshot_21\" src=\"https://github.com/user-attachments/assets/520bb69c-a1cd-404a-bdf8-a541340e699a\" style=\"border-radius: 10px;\">\n\n\n## Documentation\n\n### Model description\n\nMost 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]() or a local installation to access the GUI. <!-- TODO update link --> Further information is available in the following articles:\n\n- [AEGIS: An In Silico Tool to model Genome Evolution in Age-Structured Populations (2019)](https://www.biorxiv.org/content/10.1101/646877v1)\n- [An In Silico Model to Simulate the Evolution of Biological Aging (2016)](https://www.biorxiv.org/content/10.1101/037952v1)\n<!-- TODO including ODD as modeled by https://www.jasss.org/23/2/7.html-->\n\n### API reference\n\nExhaustive, searchable API reference made by pdoc is available [here](https://valenzano-lab.github.io/aegis/).\n\n## Contributors\n\n- **Martin Bagi\u0107** (v2): [email](martin.bagic@outlook.com), [github](https://github.com/martinbagic)\n- **Dario Valenzano** (v1, v2): [github](https://github.com/dvalenzano)\n- **Erik Boelen Theile** (v2)\n- **Arian \u0160ajina** (v1): [github](https://github.com/ariansajina)\n- **William Bradshaw** (v1): [github](https://github.com/willbradshaw)",
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