  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).
