Team:SJTU-Software/Contributions
Overview
With so many diagnosis methods developed after the start of iGEM competition, DNA computation, a newly appeared method, came into our vision. In communication with professor Da Han, an expert from Shanghai Jiaotong University in this field, we realized that traditional method are troublesome, inconvenient, and sometimes expensive.
Thus, we developed DNA computation platform, which allowed the experimenters to conduct relevant researches. The platform, which includes SVM analysis, differential expression analysis, secondary structure forecast and spurious hybridization searching, standardized the progress and increased efficiency and accuracy. Meanwhile, we have also conducted social practice for promotion of the diagnosis method and synthetic biology. Moreover, we used our platform to solve problems for other iGEM teams.
Function
Since the DNA computation is a recently developed method for areas like disease diagnosis, our project builds a standard platform for DNA computation related researches.
Our software provides a multifaceted contribution to the iGEM community. Teams following us can introduce more computing methods and add more functions to the platform, which allows DNA computing to involve more fields in future.
SVM analysis and differential expression analysis used in our software provide convenient web tools that give experimental groups a simple and highly actionable way to analyze data. The function of spurious hybridization search and secondary structure prediction can help reduce labor work in experiments involving nucleic acids.
In communication with other teams, we learned that many iGEM teams need to consider the secondary structure of nucleic acids in their experiments, such as SJTU-BioX-Shanghai, OUC-R. For instance, SJTU-BioX-Shanghai need to design structureless probes at two ends of aptazyme, and TMSD reaction is also applied in their optimization design. OUC-R's experiments are closely related to DNA cross structures, so they need to look for stem-loop structures to see if cross structures are possible. These show that our project is able to help iGEM in the future.
In general, each function in our software can deal with a specific biological problem, which is helpful for the implementation of biological experiments. We firmly believe that it will have a brilliant development prospect in the future.
Human practices
In order to improve the public's consciousness of physical health, we conducted lectures in primary and high schools. We also built an education website and designed a game about anti-cancer advocacy and synthetic biology, in hope for raising people’s awareness of cancer prevention and reduce the risk of cancer.