Acta Scientific Computer Sciences

Research Article Volume 4 Issue 7

DOSSIER: A Toolkit to Extract Data from Digital Life Simulations Using Dose

Argho Maitra1 and Maurice HT Ling1,2*

1School of Data Sciences, Perdana University, Malaysia
2HOHY Private Limited, Singapore

*Corresponding Author: Maurice HT Ling, School of Data Sciences, Perdana University, Malaysia.

Received: May 14, 2022; Published: June 09, 2022

Abstract

Artificial life, also known as digital organisms, has been useful in testing various evolutionary hypotheses. DOSE is one of the platforms for experimenting with digital organisms and had been used in several studies. However, the internal architecture of DOSE does not allow for easy processing of simulation results despite storing the state of each digital organism and the world for each generation in an SQLite database. To address this problem, we implemented DOSSIER, a Python-based toolkit that can connect with the SQLite database, facilitate data extraction and processing into a standardized table of fitness scores.


Keywords: Artificial Life; Digital Organisms; Cellular Automata; Computational Tool; Python Programming; DOSE

References

  1. Langton CG. “Studying Artificial Life with Cellular Automata”. Physica D: Nonlinear Phenomena1-3 (1986): 120-149.
  2. Lenski RE., et al. “Genome Complexity, Robustness and Genetic Interactions in Digital Organisms”. Nature6745 (1999): 661-664.
  3. Wilke CO and Adami C. “The Biology of Digital Organisms”. Trends in Ecology and Evolution11 (2002): 528-532.
  4. Yedid G and Bell G. “Microevolution in an Electronic Microcosm”. The American Naturalist5 (2001): 465-487.
  5. Adami C. “Digital Genetics: Unravelling the Genetic Basis of Evolution”. Nature Reviews Genetics2 (2006): 109-118.
  6. Wilke CO., et al. “Evolution of Digital Organisms at High Mutation Rates Leads to Survival of the Flattest”. Nature6844 (2001): 331-333.
  7. Wilke CO and Christoph A. “Interaction Between Directional Epistasis and Average Mutational Effects. Proceedings of the Royal Society of London Series B: Biological Sciences1475 (2001): 1469-1474.
  8. Grabowski LM., et al. “A Case Study of the De Novo Evolution of a Complex Odometric Behavior in Digital Organisms”. Plos One4 (2013): e60466.
  9. Gupta A., et al. “Evolution of Genome Size in Asexual Digital Organisms. Scientific Reports1 (2016): 25786.
  10. Pennock RT. “Models, Simulations, Instantiations, and Evidence: The Case of Digital Evolution. Journal of Experimental and Theoretical Artificial Intelligence1 (2007): 29-42.
  11. Castillo CF and Ling MH. “Digital Organism Simulation Environment (DOSE): A Library for Ecologically-Based In Silico Experimental Evolution”. Advances in Computer Science : An International Journal1 (2014): 44-50.
  12. Ray TS. Evolution and Optimization of Digital Organisms. Scientific Excellence in Supercomputing: The IBM 1990 Contest Prize Papers (1991).
  13. Ofria C and Wilke CO. “Avida: A Software Platform for Research in Computational Evolutionary Biology”. Artificial Life2 (2004): 191-229.
  14. Liard V., et al. “The Complexity Ratchet: Stronger than Selection, Stronger than Evolvability, Weaker than Robustness”. Artificial Life1 (2020): 38-57.
  15. Castillo CF and Ling MH. “Digital Organism Simulation Environment (DOSE) Version 1.0.4”. Current STEM, Volume 1 (Nova Science Publishers, Inc.) (2018): 1-106.
  16. Ling MH. “An Artificial Life Simulation Library Based on Genetic Algorithm, 3-Character Genetic Code and Biological Hierarchy”. The Python Papers5 (2012): 1-30.
  17. Ling MH. “Ragaraja 1.0: The Genome Interpreter of Digital Organism Simulation Environment (DOSE)”. The Python Papers Source Codes2 (2012): 1-45.
  18. Ang DG and Ling MH. “Sudden and Steep Harsh Environment Results in Over-Compensation in Digital Organisms”. EC Microbiology7 (2021): 104-113.

Citation

Citation: Argho Maitra and Maurice HT Ling. “DOSSIER: A Toolkit to Extract Data from Digital Life Simulations Using Dose". Acta Scientific Computer Sciences 4.7 (2022): 37-40.

Copyright

Copyright: © 2022 Argho Maitra and Maurice HT Ling. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.




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