DOSE Technology Papers

[1] Castillo, CFG, Ling, MHT. 2014. Digital Organism Simulation Environment (DOSE): A Library for Ecologically-Based In Silico Experimental Evolution. Advances in Computer Science: an International Journal 3(1): 44-50.

Testing evolutionary hypothesis in biological setting is expensive and time consuming. Computer simulations of organisms (digital organisms) are commonly used proxies to study evolutionary processes. A number of digital organism simulators have been developed but are deficient in biological and ecological parallels. In this study, we present DOSE (Digital Organism Simulation Environment), a digital organism simulator with biological and ecological parallels. DOSE consists of a biological hierarchy of genetic sequences, organism, population, and ecosystem. A 3-character instruction set that does not take any operand is used as genetic code for digital organism, which the 3-nucleotide codon structure in naturally occurring DNA. The evolutionary driver is simulated by a genetic algorithm. We demonstrate the utility in examining the effects of migration on heterozygosity, also known as local genetic distance.

[2] Maitra, A, Ling, MHT. 2022. DOSSIER: A Toolkit to Extract Data from Digital Life Simulations Using Dose. Acta Scientific Computer Sciences 4(7): 37-40.

Artificial life, also known as digital organisms, has been useful in testing various evolutionary hypotheses. DOSE is one of the platforms for experimenting with digital organisms and had been used in several studies. However, the internal architecture of DOSE does not allow for easy processing of simulation results despite storing the state of each digital organism and the world for each generation in an SQLite database. To address this problem, we implemented DOSSIER, a Python-based toolkit that can connect with the SQLite database, facilitate data extraction and processing into a standardized table of fitness scores.