Modes

This release introduces a new organizational structure and new features. We have organized functionality into 'modes'. The original Host and Symbiont are the 'default' mode and we have added the following additional modes: 'lysis', 'efficient', and 'pgg'.

Lysis
This mode supports functionality relevant to modeling bacteriophage/bacterial dynamics including lysis and lysogeny reproductive cycles.

Efficient
This mode supports an "efficient" symbiont, which has an efficiency value, enabling it to suffer from high mutation rates that decrease its ability to process resources.

PGG
This mode supports a public goods game between endosymbionts infecting the same host.

Additions to Default Mode
We have also added the ability for symbionts to survive outside of a host and engage in ectosymbiosis or collect resources from the environment independent of a host.

Basic Endosymbionts

This is the full release of the basic endosymbionts support.
This code supports the results found in the publication:
Anya E. Vostinar, Charles Ofria; Spatial Structure Can Decrease Symbiotic Cooperation. Artif Life 2019; 24 (4): 229–249. doi: https://doi.org/10.1162/artl_a_00273

Basic Endosymbionts

This code supports the results found in the publication:
Anya E. Vostinar, Charles Ofria; Spatial Structure Can Decrease Symbiotic Cooperation. Artif Life 2019; 24 (4): 229–249. doi: https://doi.org/10.1162/artl_a_00273