Editing Avida (software)

{{Short description|Artificial life software platform}}
{{Infobox software
| name = 
| screenshot = Avida_2.6_screenshot.png
| caption = Map tab for Avida 2.6
| author = [[Charles Ofria]], [[Chris Adami]]
| developer = [[Charles Ofria]]
| latest release version = 2.14.0
| latest release date = {{start date and age|2014|02|06}}<ref name="releases">{{cite web
  | url = https://sourceforge.net/projects/avida/
  | title = Avida Digital Life Platform download
  | website = sourceforge.net
  | date = 6 February 2014
 | access-date = 2021-03-27
}}</ref>
| operating system = [[Microsoft Windows]] 7 or later, [[macOS]] 10.8 or later, Linux / Unix.
| programming language = [[C++]], [[Objective-C]]
| genre = [[Artificial life]]
| license = [[LGPL]]
}}

'''Avida''' is an [[artificial life]] software platform to study the [[evolutionary biology]] of [[self-replication|self-replicating]] and [[evolution|evolving]] [[computer program]]s ([[digital organism]]s). Avida is under active development by [[Charles Ofria]]'s Digital Evolution Lab at [[Michigan State University]]; the first version of Avida was designed in 1993 by Ofria, [[Chris Adami]] and [https://simplystatistics.org/posts/2012-08-17-interview-with-c-titus-brown-computational-biologist/ C. Titus Brown] at [[Caltech]], and has been fully reengineered by Ofria on multiple occasions since then.  The software was originally inspired by the [[Tierra (computer simulation)|Tierra]] system.

== Design principles ==

[[Tierra (computer simulation)|Tierra]] simulated an evolutionary system by introducing computer programs that competed for computer resources, specifically processor (CPU) time and access to main memory. In this respect it was similar to [[Core Wars]], but differed in that the programs being run in the simulation were able to modify themselves, and thereby evolve. Tierra's programs were artificial life organisms.{{citation needed|date=February 2012}}

Unlike Tierra, Avida assigns every digital organism its own protected region of memory, and executes it with a separate virtual [[Central processing unit|CPU]]. By default, other digital organisms cannot access this memory space, neither for reading nor for writing, and cannot execute code that is not in their own memory space.

A second major difference is that the virtual CPUs of different organisms can run at different speeds, such that one organism executes, for example, twice as many instructions in the same time interval as another organism. The speed at which a virtual CPU runs is determined by a number of factors, but most importantly, by the ''tasks'' that the organism performs: logical computations that the organisms can carry out to reap extra CPU speed as bonus.

== Use in research ==

Adami and Ofria, in collaboration with others, have used Avida to conduct research in digital evolution, and the scientific journals ''[[Nature (journal)|Nature]]'' and ''[[Science (journal)|Science]]'' have published four of their papers.

The 2003 paper "The Evolutionary Origin of Complex Features" describes the evolution of a mathematical [[Equality (mathematics)|equal]]s [[operator (programming)|operation]] from simpler bitwise operations.<ref>{{cite journal|last1=Lenski|first1=R. E.|last2=Ofria|first2=C.|last3=Pennock|first3=R. T.|last4=Adami|first4=C.|date=2003|author1-link=Richard Lenski|author2-link=Charles Ofria|author3-link=Robert T. Pennock|author4-link=Chris Adami|title=The evolutionary origin of complex features|journal=Nature|volume=423|pages=139–144|url=http://myxo.css.msu.edu/papers/nature2003/Nature03_Complex.pdf|doi=10.1038/nature01568|pmid=12736677|issue=6936|bibcode=2003Natur.423..139L|s2cid=4401833|access-date=2012-01-30|archive-date=2021-01-21|archive-url=https://web.archive.org/web/20210121232710/http://myxo.css.msu.edu/papers/nature2003/Nature03_Complex.pdf|url-status=dead}}</ref>

==Use in education==

{{Infobox software
| name = Avida-ED
| author = [[Jeff Clune]]
| developer = [[Diane J. Blackwood]]
| latest release version = 3
| latest release date = {{start date and age|2021|10|10}}<ref name="releasesb">{{cite web
  | url = https://github.com/DBlackwood/AvidaED_user_interface
  | title = Avida-ED User Interface
  | website = github.com
  | access-date = 2021-10-11
}}</ref>
| programming language = [[C++]], [[JavaScript]]
| genre = [[Artificial life]]
| license = [[GPL]]
| website = Main: {{URL|avida-ed.msu.edu}}, Mirror: {{URL|avida-ed-mirror1.beacon-center.org}}
}}

The Avida-ED project ([https://avida-ed.msu.edu/app/AvidaED.html Avida-ED]) uses the Avida software platform within a simplified graphical user interface suitable for use in evolution education instruction at the high school and undergraduate college level, and provides freely available software, documentation, tutorials, [https://avida-ed.msu.edu/curriculum/ lesson plans], and other course materials.<ref name="SmithJohnson2016">{{cite journal|last1=Smith|first1=James J.|last2=Johnson|first2=Wendy R.|last3=Lark|first3=Amy M.|last4=Mead|first4=Louise S.|last5=Wiser|first5=Michael J.|last6=Pennock|first6=Robert T.|title=An Avida-ED digital evolution curriculum for undergraduate biology|journal=Evolution: Education and Outreach|volume=9|issue=1|year=2016|issn=1936-6426|doi=10.1186/s12052-016-0060-0|doi-access=free}}</ref><ref name="scie_Onli">{{Cite web
| title = Online tool speeds up evolution education
| author = Anonymous
| work = ScienceDaily
| date = 5 February 2018
| access-date = 3 July 2021
| url = https://www.sciencedaily.com/releases/2018/02/180205113043.htm
| quote = 
}}</ref> The Avida-ED software runs as a web application in the browser, with the user interface implemented in JavaScript and Avida compiled to JavaScript using Emscripten, making the software broadly compatible with devices commonly used in classrooms.<ref name="TaylorAuerbach2016">{{cite journal|last1=Taylor|first1=Tim|last2=Auerbach|first2=Joshua E.|last3=Bongard|first3=Josh|last4=Clune|first4=Jeff|last5=Hickinbotham|first5=Simon|last6=Ofria|first6=Charles|last7=Oka|first7=Mizuki|last8=Risi|first8=Sebastian|last9=Stanley|first9=Kenneth O.|last10=Yosinski|first10=Jason|title=WebAL Comes of Age: A Review of the First 21 Years of Artificial Life on the Web|journal=Artificial Life|volume=22|issue=3|year=2016|pages=364–407|issn=1064-5462|doi=10.1162/ARTL_a_00211|pmid=27472416 |hdl=2241/00154082|s2cid=12092129 |url=https://tsukuba.repo.nii.ac.jp/record/48596/files/AL_22-3.pdf |hdl-access=free}}</ref> This approach has been shown to be effective in improving students' understanding of evolution.<ref name="PennockSmith2018">{{cite journal|last1=Pennock|first1=Robert T.|last2=Smith|first2=James J.|last3=Mead|first3=Louise S.|last4=Richmond|first4=Gail|last5=Lark|first5=Amy|title=Exploring the Relationship between Experiences with Digital Evolution and Students' Scientific Understanding and Acceptance of Evolution|journal=The American Biology Teacher|volume=80|issue=2|year=2018|pages=74–86|issn=0002-7685|doi=10.1525/abt.2018.80.2.74|s2cid=52260399 }}</ref><ref name="Abi AbdallahFonner2020">{{cite journal|last1=Abi Abdallah|first1=Delbert S.|last2=Fonner|first2=Christopher W.|last3=Lax|first3=Neil C.|last4=Babeji|first4=Matthew R.|last5=Palé|first5=Fatimata A.|title=Evaluating the Use of Avida-ED Digital Organisms to Teach Evolution & Natural Selection|journal=The American Biology Teacher|volume=82|issue=2|year=2020|pages=114–119|issn=0002-7685|doi=10.1525/abt.2020.82.2.114|doi-access=free}}</ref><ref name="PennockRichmond2014">{{cite journal|last1=Pennock|first1=Robert T.|last2=Richmond|first2=Gail|last3=Lark|first3=Amy|title=Modeling Evolution in the Classroom|journal=The American Biology Teacher|volume=76|issue=7|year=2014|pages=450–454|issn=0002-7685|doi=10.1525/abt.2014.76.7.6|s2cid=83720929 }}</ref>
The Avida-ED project was the winner of the 2017 International Society for Artificial Life Education and Outreach Award.<ref name="alif_2017">{{Cite web
| title = 2017 ISAL Awards: Winners - Artificial Life
| last = Taylor | first = Tim
| work = Artificial Life
| date = 16 September 2017
| access-date = 3 July 2021
| url = https://alife.org/2017-isal-awards-winners/
| quote = 
}}</ref>

==See also==
{|
|
*[[Artificial life]]
*[[Digital organism]]
*[[Digital organism simulators]]
*[[Darwinbots]]
|
*[[Tierra (computer simulation)|Tierra]]
*[[Conway's Game of Life]]
*[[Nanopond (software)|Nanopond]]
*[[Aevol]]
|}

==References==
*[http://carlzimmer.com/articles/2005.php?subaction=showfull&id=1177184710&ucat=8 "Testing Darwin"], [[Discover Magazine]], February 2005.
{{reflist}}

== External links ==
*[https://github.com/devosoft/avida Avida Software - GitHub]
*[http://avida-ed.msu.edu Avida-ED Project - Robert T. Pennock]
*[https://web.archive.org/web/20071101065234/http://www.programerror.com/software/avida/ An Avida Developer's Site]
*[https://devolab.org/?s=AVida MSU Devolab website]

===Scientific publications featuring Avida===
* C. Adami and C.T. Brown (1994), Evolutionary Learning in the 2D Artificial Life Systems  Avida, in: R. Brooks, P. Maes (Eds.), Proc. Artificial Life IV, MIT Press, Cambridge, MA, p.&nbsp;377-381. {{arXiv|adap-org/9405003}}
* [[R. E. Lenski]], C. Ofria, T. C. Collier, C. Adami (1999). Genome Complexity, Robustness, and Genetic Interactions in Digital Organisms.  ''Nature'' '''400:'''661-664.
* C.O. Wilke, J.L. Wang, C. Ofria, R.E. Lenski, and C. Adami (2001). Evolution of Digital Organisms at High Mutation Rate Leads To Survival of the Flattest. ''Nature'' '''412:'''331-333.
* R.E. Lenski, C. Ofria, R.T. Pennock, and C. Adami (2003). The Evolutionary Origin of Complex Features. ''Nature'' '''423:'''139-145.
* S.S. Chow, C.O. Wilke, C. Ofria, R.E. Lenski, and C. Adami (2004). Adaptive Radiation from Resource Competition in Digital Organisms. ''Science'' '''305:'''84-86.
* J. Clune, D. Misevic, C. Ofria, R.E. Lenski, S.F. Elena, and R. Sanjuán. Natural selection fails to optimize mutation rates for long-term adaptation on rugged fitness landscapes. PLoS Computational Biology 4(9): 2008. {{doi|10.1371/journal.pcbi.1000187|doi-access=free}}
* Clune J, Goldsby HJ, Ofria C, and Pennock RT (2011) Selective pressures for accurate altruism targeting: Evidence from digital evolution for difficult-to-test aspects of inclusive fitness theory. Proceedings of the Royal Society. [https://www.msu.edu/~jclune/webfiles/publications/Clune-2011-InclusiveFitness-Proc.Royal.Society.pdf pdf] ([https://web.archive.org/web/20111207001544/https://www.msu.edu/~jclune/webfiles/publications/Clune-2011-InclusiveFitness-Proc.Royal.Society.pdf archive])
* Benjamin E. Beckmann, Philip K. McKinley, Charles Ofria (2007). Evolution of an adaptive sleep response in digital organisms. ''ECAL 2007'' [https://web.archive.org/web/20100213012528/http://www.cse.msu.edu/notables/images/ecal-2007-sleep.pdf pdf]

[[Category:Artificial life]]
[[Category:Artificial life models]]
[[Category:Digital organisms]]