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Team:USTC Software/WhatOverview
From 2009.igem.org
One goal of synthetic biology is to understand the exciting biological phenomenon by reconstructing the systems that have the similar behavior to native.The design process is always very difficult for the biologists as the only information is the desired phenotype.Even the general system are improved to meet the requirement, the choices of reactors and the stability of the system are still problems for the experimentalists.Here we are trying to use the computer instead of the human brain to do the design process.
GOAL
The ultimate goal of our program is to assist the experimentalists to design the plasmid that works as the requirement. For example, if an oscillator behavior is the requirement as the input of the software, then the output in our imagination is a DNA sequence which works as an oscillator in E.coli or other specific biology. It is only an imagination that we have a long way to go.So,as the first goal,the output we are trying to do for the software is a network which can stably work as the requirement.Generally, the desired phonetype is the input of the software, and, optionally, the restrictions extracted from the other experiments or from the condition can be the input at the same time. And the output is a list of networks that have the similar phenotypes to the requirement,with the information of the value of parameters and the sensitivities. The ultimate goal of synthetic biology is to program complex biological networks that could achieve desired phenotype and produce significant metabolites in purpose of real world application, by fabricating standard components from an engineering-driven perspective. This project explores the application of theoretical approaches to automatically design synthetic complex biological networks with desired functions defined as dynamical behavior and input-output property. We propose a novel design scheme highlighted in the notion of trade-off that synthetic networks could be obtained by a compromise between performance and robustness. Moreover, series of eligible strategies, which consist of various topologies and possible standard components such as BioBricks, provide multiple choices to facilitate the wet experiment procedure. Description of all feasible solutions takes advantage of SBML and SBGN standard to guarantee extensibility and compatibility.
