Prcell: Sentetik Biyoloji için Sinyal Yolağı Programlamaya Yönelik Bir Yazılım

Abstract

Synthetic biology is a new and interdisciplinary field of research aimed at applying the fundamental principles of engineering to biology, especially to the cell. It aims to design and produce artificial biological systems. Synthetic biology is very important to for design or adjust new signaling pathways that can be designed and implemented to alter or correct cellular functions, enable the cell to respond to environmental conditions, or manage cellular development. Researchers expect a future in which the design of biological circuits will resemble the design of integrated circuits in electronics and increase the capabilities of genetic engineering. The purpose of the applications developed as a cell programming language is to design genetic circuits for living cells and to realize the designed genetic circuit in the cell. One of these is Cello, which is based on the electronic circuit design program, verilog, and uses logic gates to design electronic circuits. Since we think that the application of electronic circuit design logic to biological circuits cannot be enough, in this thesis we have developed a new programming language for designing biological circuits which we call prCell. The main feature of prCell is that instead of the logic gates used for any electronic circuit design to design the biological circuit, it has a logic based on the dynamic structures in which the user will determine the input-output and control objects. This provides flexibility and possibility to design a very large and complex biological circuit. Since there will be a membership system in prcell to be published over the internet, there will be a database of the user and a biological circuit design environment of the user. Our most important goal is that anyone interested in synthetic biology can easily and effectively design the signal pathway and apply it in the living cell. We believe that in order to better model intracellular events, prcell will be developed according to user demands and will provide a different perspective for reprogramming living things.