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 except space (to prevent confusion) as possible bases. This will give 830,584 3-character codons, which represents nearly 13 thousand times genomic compression. This means that the genome of Escherichia coli (a common experimental bacterium in biology with 4.6 million bases) can be represented by about 360 codons of 94 bases or a chromosome of 1080 bases.

• Organism, and Population

An organism (DO) is an encapsulation of its genome and the status of the organism (see Genome and Status of an Organism for details). One or more organisms will make up a population. Population(s) is one of the two simulation entries of DOSE. Hence, at the simplest, a population can be just one organism with one chromosome as its genome.

• Ecosystem and World

A world is an encapsulation of an ecosystem and a set of operations on the ecosystem (see DOSE World for details). An ecosystem is made up of one or more ecological cells, which is a quantum of space. All organisms within the same ecological cell are deemed to be within the same space. Movement of organisms is defined as a change in ecological cell. However, the organisms do not reside within the ecosystem, instead each organism is mapped onto one ecological cell. This means that each organism has to be aware of their own location by means of their organism status. The state of each ecological cell is defined as a list of 4 elements.

• Mutations

• Gene Expression

• Multi-populations

• Deme

• Deployment

• Fitness

• Mating