Nothing Special   »   [go: up one dir, main page]

skip to main content
article

Avida: a software platform for research in computational evolutionary biology

Published: 01 April 2004 Publication History

Abstract

Avida is a software platform for experiments with self-replicating and evolving computer programs. It provides detailed control over experimental settings and protocols, a large array of measurement tools, and sophisticated methods to analyze and post-process experimental data. We explain the general principles on which Avida is built, as well as its main components and their interactions. We also explain how experiments are set up, carried out, and analyzed.

References

[1]
1. Adami, C., Brown, C. T., & Haggerty, M. R. (1995). Abundance distributions in artificial life and stochastic models: "Age and area" revisited. Lecture Notes in Artificial Intelligence, 929, 503-514.
[2]
2. Adami, C., Ofria, C., & Collier, T. C. (2000). Evolution of biological complexity. Proceedings of the National Academy of Sciences of the U.S.A., 97, 4463-4468.
[3]
3. Barton, N., & Zuidema, W. (2003). Evolution: The erratic path towards complexity. Current Biology, 13, R649-R651.
[4]
4. Chu, J., & Adami, C. (1997). Propagation of information in populations of self-replicating code. In C. G. Langton & T. Shimohara (Eds.), Proceedings of Artificial Life V (pp. 462-469). Cambridge, MA: MIT Press.
[5]
5. Cooper, T., & Ofria, C. (2002). Evolution of stable ecosystems in populations of digital organisms. In R. K. Standish, M. A. Bedau, & H. A. Abbass (Eds.), Proceedings of Artificial Life VIII (pp. 227-232). Cambridge, MA: MIT Press.
[6]
6. Darwin, C. (1859). On the origin of species by means of natural selection. London: Murray.
[7]
7. Dennett, D. (2002). The new replicators. In M. Pagel (Ed.), Encyclopedia of evolution (pp. E83-E92). Oxford, UK: Oxford University Press.
[8]
8. Dewdney, A. K. (1984). In a game called core war hostile programs engage in a battle of bits. Scientific American, 250(4), 14-22.
[9]
9. Egri-Nagy, A., & Nehaniv, C. L. (2003). Evolvability of the genotype-phenotype relation in populations of self-replicating digital organisms in a Tierra-like system. Lecture Notes in Artificial Intelligence, 2801, 238-247.
[10]
10. Elena, S. F., & Lenski, R. E. (2003). Evolution experiments with microorganisms: The dynamics and genetic bases of adaptation. Nature Reviews Genetics, 4, 457-469.
[11]
11. Kim, Y., & Stephan, W. (2003). Selective sweeps in the presence of interference among partially linked loci. Genetics, 164, 389-398.
[12]
12. Lenski, R. E., Ofria, C., Pennock, R. T., & Adami, C. (2003). The evolutionary origin of complex features. Nature, 423, 129-144.
[13]
13. McVean, G. A. T., & Charlesworth, B. (2000). The effects of Hill-Robertson interference between weakly selected mutations on patterns of molecular evolution and variation. Genetics, 155, 929-944.
[14]
14. O'Neill, B. (2003). Digital evolution. PLoS Biology, 1, 011-014.
[15]
15. Orr, H. A. (2000). The rate of adaptation in asexuals. Genetics, 155, 961-968.
[16]
16. Rasmussen, S., Knudsen, C., Feldberg, R., & Hindsholm, M. (1990). The coreworld--Emergence and evolution of cooperative structures in a computational chemistry. Physica D, 75, 1-3.
[17]
17. Ray, T. S. (1992). An approach to the synthesis of life. In C. G. Langton, C. Taylor, J. D. Farmer, & S. Rasmussen (Eds.), Proceedings of Artificial Life II (p. 371). Reading, MA: Addison-Wesley.
[18]
18. Travisano, M., & Rainey, P. B. (2000). Studies of adaptive radiation using model microbial systems. American Naturalist, 156, S35-S44.
[19]
19. Wilke, C. O. (2002). Maternal effects in molecular evolution. Physical Review Letters, 88, 078101.
[20]
20. Wilke, C. O., & Adami, C. (2002). The biology of digital organisms. Trends in Ecology & Evolution, 17, 528-532.
[21]
21. Wilke, C. O., Wang, J. L., Ofria, C., Lenski, R. E., & Adami, C. (2001). Evolution of digital organisms at high mutation rates leads to survival of the flattest. Nature, 412, 331-333.
[22]
22. Yedid, G., & Bell, G. (2001). Microevolution in an electronic microcosm. American Naturalist, 157, 465-487.
[23]
23. Yedid, G., & Bell, G. (2002). Macroevolution simulated with autonomously replicating computer programs. Nature, 420, 810-812.

Cited By

View all
  • (2023)Drivers of Replicator Organisation in the Nanopond Artificial ChemistryProceedings of the Companion Conference on Genetic and Evolutionary Computation10.1145/3583133.3590572(147-150)Online publication date: 15-Jul-2023
  • (2023)Matchmaker, matchmaker, make me a match: geometric, variational, and evolutionary implications of criteria for tag affinityGenetic Programming and Evolvable Machines10.1007/s10710-023-09448-024:1Online publication date: 24-Mar-2023
  • (2021)Trends in Integration of Vision and Language ResearchJournal of Artificial Intelligence Research10.1613/jair.1.1168871(1183-1317)Online publication date: 10-Sep-2021
  • Show More Cited By

Recommendations

Comments

Please enable JavaScript to view thecomments powered by Disqus.

Information & Contributors

Information

Published In

cover image Artificial Life
Artificial Life  Volume 10, Issue 2
April 2004
112 pages
ISSN:1064-5462
EISSN:1530-9185
Issue’s Table of Contents

Publisher

MIT Press

Cambridge, MA, United States

Publication History

Published: 01 April 2004

Author Tags

  1. digital organisms
  2. experimental evolution
  3. self-replicating computer programs

Qualifiers

  • Article

Contributors

Other Metrics

Bibliometrics & Citations

Bibliometrics

Article Metrics

  • Downloads (Last 12 months)0
  • Downloads (Last 6 weeks)0
Reflects downloads up to 17 Dec 2024

Other Metrics

Citations

Cited By

View all
  • (2023)Drivers of Replicator Organisation in the Nanopond Artificial ChemistryProceedings of the Companion Conference on Genetic and Evolutionary Computation10.1145/3583133.3590572(147-150)Online publication date: 15-Jul-2023
  • (2023)Matchmaker, matchmaker, make me a match: geometric, variational, and evolutionary implications of criteria for tag affinityGenetic Programming and Evolvable Machines10.1007/s10710-023-09448-024:1Online publication date: 24-Mar-2023
  • (2021)Trends in Integration of Vision and Language ResearchJournal of Artificial Intelligence Research10.1613/jair.1.1168871(1183-1317)Online publication date: 10-Sep-2021
  • (2021)X-AevolProceedings of the Genetic and Evolutionary Computation Conference Companion10.1145/3449726.3463195(1317-1325)Online publication date: 7-Jul-2021
  • (2021)Video Games as a Testbed for Open-Ended Phenomena2021 IEEE Conference on Games (CoG)10.1109/CoG52621.2021.9619042(1-9)Online publication date: 17-Aug-2021
  • (2021)Tim Taylor and Alan Dorin: Rise of the self-replicators—early visions of machines, AI and robots that can reproduce and evolveGenetic Programming and Evolvable Machines10.1007/s10710-021-09398-522:1(141-145)Online publication date: 1-Mar-2021
  • (2021)EvoCraft: A New Challenge for Open-EndednessApplications of Evolutionary Computation10.1007/978-3-030-72699-7_21(325-340)Online publication date: 7-Apr-2021
  • (2020)The Surprising Creativity of Digital EvolutionArtificial Life10.1162/artl_a_0031926:2(274-306)Online publication date: 1-May-2020
  • (2019)Why open-endedness mattersArtificial Life10.1162/artl_a_0029425:3(232-235)Online publication date: 1-Aug-2019
  • (2019)Evolutionary innovations and where to find themArtificial Life10.1162/artl_a_0029025:2(207-224)Online publication date: 1-May-2019
  • Show More Cited By

View Options

View options

Media

Figures

Other

Tables

Share

Share

Share this Publication link

Share on social media