Configuration files and bash scripts used in the following study: "The genotype-phenotype map of an evolving digital organism", published in PLoS Computational Biology (2017).
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merely_viable_organisms
README.md
The genotype-phenotype map of an evolving organism.pdf
avida
avida.cfg
bash_script_directional_selection_process.sh
bash_script_purifying_selection_process.sh
bash_script_random_exploration_genotype_network.sh
convert_seq_into_org.sh
environment_directional_selection_process.cfg
environment_purifying_selection_process.cfg
environment_random_exploration_genotype_space.cfg
events.cfg
instructions.txt
instset-heads.cfg
merely_viable_sequences.txt
random_genotypes
random_genotypes.c
random_genotypes.sh

README.md

The genotype-phenotype map of an evolving digital organism.

Configuration files and bash scripts used in this study:

Avida version 2.14.0

Configuration files required

  • avida.cfg (the Avida default file was used and some configuration options were modified when Avida was executed in standard and analyze modes).
  • events.cfg (renamed when running the directional selection process).
  • environment.cfg (renamed when running the three different process indicated below).
  • instset-heads.cfg
  • avida (executable: compiled for amd64).

The database was generated following these three steps:

1. Random exploration of genotype space

files provided:

  • random_genotypes.c (source file).
  • random_genotypes (compiled for amd64 from the source file).
  • random_genotypes.sh
  • bash_script_random_exploration_genotype_network.sh

execution:

./random_genotypes.sh # it generates 10000 random genotypes that are stored in the output file "rand_seq.txt".
./bash_script_random_exploration_genotype_network.sh # it takes those random genotypes and check viability and phenotype in analyze mode.

2. Directional selection process

files provided:

  • merely_viable_sequences.txt (1000 genotypes corresponding to merely viable organisms resulting from the exploration of genotype space)
  • convert_seq_into_org.sh (translates a genotype into an organism's file)
  • instructions.txt (it maps the letters from a genotype to the instructions specified in the instruction set file "instset-heads.cfg")
  • merely_viable_organisms (folder containing 1000 merely viable organisms resulting from the random exploration of genotype space).
  • bash_script_directional_selection_process.sh

execution:

./convert_seq_into_org.sh # it takes the genotypes, creates one organism'file per genotype, and store them (merely viable organisms folder)
./bash_script_directional_selection_process.sh # it finds and selects randomly one genotype having a distinct phenotype using "ancestor_1.org" (from the "merely_viable_organisms" folder) as the seed of the evolutionary process.

3. Purifying selection process

files provided:

bash_script_purifying_selection_process.sh

execution:

./bash_script_purifying_selection_process.sh # it performs a double-mutant random walk (i.e., it replaces two instructions at a time) while keeping viability and phenotype, starting from a specific sequence (as an example).