C Library for Simulated Evolution of Biological Networks

TL;DR

This paper introduces a versatile, open-source C library that facilitates the simulation and evolution of biological networks, enabling researchers to easily perform experiments in network evolution and function.

Contribution

It provides a comprehensive, cross-platform library with genetic algorithms and simulation functions specifically designed for biological network evolution research.

Findings

Library supports genetic algorithms for various network types

Enables easy simulation and evolution of biological networks

Open source with GUI and cross-platform compatibility

Abstract

Simulated evolution of biological networks can be used to generate functional networks as well as investigate hypotheses regarding natural evolution. A handful of studies have shown how simulated evolution can be used for studying the functional space spanned by biochemical networks, studying natural evolution, or designing new synthetic networks. If there was a method for easily performing such studies, it can allow the community to further experiment with simulated evolution and explore all of its uses. As a result, we have developed a library written in the C language that performs all the basic functions needed to carry out simulated evolution of biological networks. The library comes with a generic genetic algorithm as well as genetic algorithms for specifically evolving genetic networks, protein networks, or mass-action networks. The library also comes with functions for simulating these networks. A user needs to specify a desired function. A GUI is provided for users to become oriented with all the options available in the library. The library is free and open source under the BSD lisence and can be obtained at evolvenetworks.sourceforge.net. It can be built on all major platforms. The code can be most conveniently compiled using cross-platform make (CMake).