Avida “Reassignment of instruction sets using digital evolution.”
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Transcript of Avida “Reassignment of instruction sets using digital evolution.”
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AVIDA“REASSIGNMENT OF INSTRUCTION SETS USING DIGITAL EVOLUTION.”
Bianca BullockScott Harrison
Alex Ropelewski
Bienvenido Velez
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SOFTWARE ENGINEERING Modifying the source code of the software How to control the code in other directions?
Original
1000 generations
Clone 1001-2000
S.P.1001-2000
CODON REASSINGMENT Which codes are we trying to modify? What is IOIO
AUG|GUG|UGA UAA UAG
Stop codons
Mukai, T., Hayashi, A., Iraha, F., Sato, A., Ohtake, K., Yokoyama, S., & Sakamoto, K. (2010). Codon reassignment in the Escherichia coli genetic code. Nucleic acids research, 38(22), 8188-8195.http://nar.oxfordjournals.org/content/38/22/8188.full
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HOW DO WE MONITOR AND SUPERCOMPUTE AVIDA EVOLUTION?
Which AVIDA organism is better and why? What happened and when?
Ancestor organismOrganism fromgeneration 483
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RUNNING AVIDA
Blacklight Writing a recursive script Parallel instead of serial processing of
multiple replicate Avida experiments
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ALTERING AVIDA
What is the purpose of altering the Avida source code?
What is the purpose of identifying the phenotype of an organism?
Why are we minimizing runtime?
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ACKNOWLEDGEMENTS
Pat Sudac (PSC) Alex Ropelewski (PSC) Pallavi Ishwad (PSC) Luis Vázquez-Quiñones (PSC) Hugh Nicholas (PSC) Scott Harrison (NCAT) Robert Newman (NCAT) Bienvenido Velez (UPRM)