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davidrmiller / biosim4

Biological evolution simulator
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Publish scientific article on Biosim? #71

Open petterreinholdtsen opened 2 years ago

petterreinholdtsen commented 2 years ago

Learning about Biosim4 reminded me of the Tierra system from thirty years ago, and made me hope you will publish your experiences with it as a scientific paper to make sure your ideas are conserved and recognized also when Youtube is long gone.

Are you aware of the Tierray system? You can read more about it in https://en.wikipedia.org/wiki/Tierra_(computer_simulation) , https://faculty.cc.gatech.edu/~turk/bio_sim/articles/tierra_thomas_ray.pdf , https://www.nytimes.com/1991/08/27/science/lively-computer-creation-blurs-definition-of-life.html , https://www.mediamatic.net/en/page/9047/tierra and https://yewtu.be/watch?v=Wl5rRGVD0QI .

davidrmiller commented 2 years ago

I was not aware of Tierra, what an interesting project. I especially admire the "jump to template" feature in their instruction set -- brilliant. Thanks for the pointer.

SrGuille commented 2 years ago

Hi, I am planning to do my final project of my computer science degree about Biosim4. I was wondering if you based your work in some previous one (papers, studies...), as it is a requirement to have those sources. Thanks in advance, I love your work!

davidrmiller commented 2 years ago

Hi Guillermo, My main source of inspiration was Richard Dawkins' book The Selfish Gene:

Dawkins, R. (2006). The Selfish Gene. Oxford University Press.

After I wrote the biosim4 simulator, I learned about a few other genetic simulators that were similar. One of them is the Tierray system as @petterreinholdtsen mentioned above. I'm sorry I have lost the references to the others.

A quick google search produced these references that might or might not be relevant:

Dalquen, D. A., Anisimova, M., Gonnet, G. H., & Dessimoz, C. (2011). “ALF—a simulation framework for Genome Evolution.” Molecular Biology and Evolution, 29(4), 1115–1123. https://doi.org/10.1093/molbev/msr268. https://pdfs.semanticscholar.org/7a15/48eae599fa5c61427e5b5bffd42e1421c4a9.pdf.

Baumdicker, Franz, et al. “Efficient Ancestry and Mutation Simulation With Msprime 1.0.” Genetics, edited by S Browning, vol. 220, no. 3, Oxford UP (OUP), Dec. 2021. Crossref, https://doi.org/10.1093/genetics/iyab229.

It's a fascinating area of study. Wishing you smooth success in completing that degree.