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  Topic: Evolutionary Computation, Stuff that drives AEs nuts< Next Oldest | Next Newest >  

Posts: 1377
Joined: June 2008

(Permalink) Posted: June 13 2009,00:12   

Quote (Wesley R. Elsberry @ June 12 2009,23:07)
I'll check with Reed Cartwright about existing popgen packages.

Avida is not a package that aims to directly model biological population genetics. There is quite a lot of conceptual overlap between Avida evolution and biological evolution, but it isn't at the low-level that MA claims to operate at. For example, current research in Avida is looking at the role of compensatory mutations. But each mutation in an Avidian is an instruction, not a base as in DNA. The Avida research can provide another line of evidence that complements that of biological research on compensatory mutations, but it isn't aimed at answering questions like, "At what rate should we expect compensatory mutations to fix in species X?" It's that kind of question that the folks pushing MA position it as a tool to answer, or would if they took any note of compensatory mutations at all. I think you get the drift, though.

Avida, by the way, has no difficulty in cranking out data on generation after generation for a set population size. Most Avida work is done on population sizes between 900 and 10,000 Avidians. However, I'm working on extending the Avida-ED program, and one part is to allow up to 90,000 organisms in the population. That is, by the way, accomplished with a change to the graphical user interface to allow selection of a grid size of up to 300 by 300, where the current version's grid-size slider only goes up to 100. The underlying Avida instance is unchanged. Tracking mutations is possible in Avida as well, but is done in analysis after the run finishes. Runs can go into the millions of updates. I don't know that anyone has tried to find an upper limit. Avida's ability to do this is because it only needs to hold the current population and grid in memory. Everything else gets written to disk.

Umm, what happened to Model-View-Controller? The idea that the model is costrained by the UI is pretty scary.

Iím referring to evolution, not changes in allele frequencies. - Cornelius Hunter
Iím not an evolutionist, Iím a change in allele frequentist! - Nakashima

  419 replies since Mar. 17 2009,11:00 < Next Oldest | Next Newest >  

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