Main Concepts in DOSE

There are a couple of concepts in DOSE that are necessary to grasp before writing a simulation.

• Bases, Chromosomes, and Genome: A genome is the entire set of genes for an organism and it can be in one or more chromosomes. The genetic alphabets that made up a gene are known as bases. In biology, the number of chromosomes in an organism can vary from 1 (most bacteria) to as many as 1260 (a fern known as Adder's-Tongue, with the largest number of chromosomes known to date), and the size of genome can range from 160 thousand bases (Carsonella ruddi, a bacterium) to 149 billion bases (Paris japonica, a rare Japanese flower).

As the genome size is a memory allocation, it is rarely that digital organisms (DO) will contain a genome size comparable to even the smallest known genome (Carsonella ruddi) as it will use up at least 160 KB per genome. To simulate the genome of Paris japonica will take 149 MB of memory per genome. However, simulating large genomes can be accomplished using compression. In biology, only 4 bases are used - A, T, C, and G. It is like writing with only 4 alphabets. Three consecutive bases/alphabets is known as a codon; hence, there are 64 codons (4**3 = 64). Although it is common that DO uses binary genome (2 bases) or integer genome (10 bases), it is possible to use all of the 94 ASCII printable characters (that is, !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_abcdefghijklmnopqrstuvwxyz{|}~`) except space (to prevent confusion) as possible bases.

• Organism, and Population:

• Ecosystem and World:

• Mutations:

• Gene Expression:

• Multi-populations:

• Deme:

• Deployment:

• Fitness:

• Mating: