mpi-age-aegis 1.0

AEGIS - Ageing of Evolving Genomes In Silico

AEGIS

Ageing of Evolving Genomes In Silico

A highly versatile discrete numerical model of genome evolution - both sexual and asexual - for a population of agents whose fitness parameters are encoded age-specifically in bit arrays which are free to evolve due to mutation and recombination.

This is a software implementation of the model described in this article in section "The Model".

Who uses AEGIS?

• Valenzano Lab

Features

AEGIS can:

• simulate genome evolution in age-structured populations under a variety of evolutionary constraints
• simulate both asexually and sexually reproducing populations
• output simulation objects using pickle
• output recorded statistics to a csv
• generate figures from recorded statistics
• run a simulation until the population has reached evolutionary equilibrium (i.e. the genetic constitution is not expected to change anymore)

Installation

Since aegis has dependencies, you might want to put the installation in an isolated Python environment with virtualenv. To install just do:

pip install mpi-age-aegis

Usage

A detailed usage tutorial with examples is provided on our GitHub page.

Related articles

• An In Silico Model to Simulate the Evolution of Biological Aging

Team

• Arian Šajina ([e-mail])
• William Bradshaw ([e-mail])
• Dario Valenzano ([e-mail])

Licensing

This project is licensed under MIT license.

Acknowledgments

This project is developed in the Valenzano Lab of the Max Planck Institute for Biology of Ageing, Cologne. We thank all the lab members and friends of the lab for their constructive comments and suggestions.