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Life is fascinating and deeply intriguing. Despite so, life forms on Earth or carbon-based life forms as a group is just one form, one possible sample of possibly a whole magnitude of life. Even then, there are many aspects of life that cannot be deciphered even by examining current life forms; for example, how did chemical reactions organize themselves into biochemical pathways? How did life start? How is intelligence formed?

To answer such questions, we will have to restart our evolutionary time to the very beginning - clearly an impossibly gargantuan task. At the same time, studying biological/carbon-based life forms is expensive, time consuming and destructive. As a molecular biologist, there is no way I can examine the entire genome of even a bacteria in an inanimate state, then somehow allow it to continue living as if time had just stopped while I am examining it.

However, if I can simulate a bacteria or any life form in a computer, then I can make a digital copy of the bacterium, pull it apart to study it while the original bacterium continues "living" in my virtual world without even knowing that it had been duplicated. Many biologists thought of virtual life forms as a new way to learn about life itself. Studying of virtual life forms is known as Artificial Life and I term "virtual life forms" as "digital organisms". There are several advantages in experimenting using digital organisms. Firstly, generation time can be much faster compared to most biological life. Secondly, it is usually cheaper to examine computer simulations than working on actual biological life. Perhaps the most important advantage of looking at life from this perspective is that by recreating life in a different medium, we are not limited to our own system of carbon-based life; hence, studying life as what-it-could-be.

Digital Organisms Simulation Environment (DOSE) is essentially a virtual world simulator for studying digital organisms. I will argue that digital organisms are considered living organisms (Koh and Ling, 2013). Despite so, being a molecular biologist by training, I have a hard time mapping components of digital organisms into biological life whenever such components are too abstract. Hence, I decided to design an artificial life / digital organism simulator that bears resemblance to biological life and ecology.

Contents

• Obtaining and Installing DOSE
• Completed Feature List
• Development Roadmap
• Using DOSE
  • Main Concepts in DOSE
  • Genome and Status of an Organism
  • DOSE World
  • What Happens in a Simulation?
  • How to Write a Simulation?
  • Examples and Case Studies
• Videos on DOSE
• DOSE Platform and Technologies
  • Foundational Papers on DOSE
  • DOSE Technology Papers
• Advanced Topics
• Studies using DOSE

License

Unless otherwise specified, dose.copads package will be licensed under Python Software Foundation License version 2; all other files will be licensed GNU General Public License version 3.

Authors

• Maurice HT Ling
• Clarence FG Castillo

Module documentation for for latest releases is found in code repository - module_documentation folder. Please download or fork DOSE repository to access the documentation as it will be in your downloaded or pulled (from forking DOSE repository) folder.