Avida Resources

Avida is an artificial life software package allowing for research into evolutionary processes using digital organisms. Avida was first coded in the 1990s, and has developed through numerous versions since then. The software is freely available for multiple platforms, including Unix, Mac OS X, and Windows.

This page is meant as a repository of my personal notes on Avida resources. As such, this is not now and likely never will be a finished document; it will be revised as I am able to incorporate materials and add my own commentary to it.

About Avida

Avida Publications (old site)
A useful but incomplete list of publications related to Avida. Various of the links do not work.
Avida publications (new site)
Listed publications can be sorted by title, first author, or year.
Publications page for Charles Ofria
A useful page listing many publications related to Avida, and most if not all the links work.

Avida Publications

This may be redundant, but I will list some Avida publications where the full text is freely available and append some summaries as I have time. Primarily taking bibliographic entries from Prof. Ofria’s page.

Lenski et al. 2003, Nature, The evolutionary origin of complex features
Experiments with Avida show how complex features can be acquired via evolutionary processes gradually building that complexity. The experiments demonstrate that some critical changes can, in fact, be deleterious on first appearance.

Misevic D, Ofria C, and Lenski RE. 2005. Sexual reproduction reshapes the genetic architecture of digital organisms. Proceedings of the Royal Society of London: Biological Sciences.

Chow S, Wilke CO, Ofria C, Lenski RE, and Adami C. 2004. Adaptive Radiation from Resource Competition in Digital Organisms. Science 305:84-86.

Ofria C and Wilke CO. 2004. Avida: A Software Platform for Research in Computational Evolutionary Biology. Journal of Artificial Life, 10:191-229.

Ofria C, Adami C, and Collier TC. 2003. Selective Pressures on Genomes in Molecular Evolution. J. theor. Biology 222:477-483.

Ofria C, Adami C, and Collier TC. 2002. Design of Evolvable Computer Languages.
IEEE Transactions in Evolutionary Computation 17:528-532.

Wilke CO, Wang J, Ofria C, Adami C, and Lenski RE. 2001. Evolution of Digital Organisms at High Mutation Rate Leads To Survival of the Flattest. Nature, 412:331-333.

Huang W, Ofria C, and Torng E. 2004. Measuring Biological Complexity in Digital Organisms. Proceedings of the Ninth International Conference on Artificial Life (p. 315-321), Boston MA, Sept 12-15.

Goings S, Clune J, Ofria C, and Pennock R. 2004. Kin Selection: The Rise and Fall of Kin-Cheaters. Proceedings of the Ninth International Conference on Artificial Life (p. 303-308), Boston MA, Sept 12-15.

Misevic D, Lenski RE, and Ofria C. 2004. Sexual reproduction and Muller’s ratchet in digital organisms. Proceedings of the Ninth International Conference on Artificial Life (p. 340-345), Boston MA, Sept 12-15.

Cooper T and Ofria C. 2002. Evolution of stable ecosystems in populations of digital organisms. Eighth International Conference on Artificial Life pp. 227-232. Dec 9-13, Sydney NSW Australlia, Russell K. Standish, Mark A. Bedau and Hussein A. Abbass (eds.).

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