Team:SYSU-Software/Implementation

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Proposed implementation

Q: Who are your proposed end users?

A: We hope our project will eventually be used not only by synthetic biologists, but also by wet lab and bioinformatics researchers, professors who teach bioinformatics, or evenand anyone who is interested in biology. Our project is designed primarily to solve the problem of thein pathwaycircuit design process for synthetic biologists. Users can firstly use our software to conduct their early design, including Topological structure of functional genetic circuits and acquisition of some parts recommended by our Transcriptional Regulation database automatically. ,Then, they may use our search module to check and find more validated information about the parts and circuits from literature. but Aat the same time, wet lab researchers can use our software to simulate a certain metabolic pathwaygenetic circuit, so as to reduce the number of rounds for their experimental verificationcircuit optimization. Additionally, those who are not major in biology can also use our software to engineer a metabolic pathway by using parts or circuits, and explore the various and amazing chemical reactions taken part in the creatures.try the procedure of building a synthetic circuit.

One of the questions in our questionnaire which shows what is the most urgent question our software needs to solve. The problems encountered in synthetic biology experiments and the urgency to be solved. Among which how to improve the expression of pathway is considered to be the most urgent problem.

The result shows that many of interviewees need our software to provide them with experimental improvement suggestions.

Q: What are the safety aspects you would need to consider?

A: In terms of safety, we need to remind our users not to misuse our software and cause biosafety issues. We should also consider user information safety and intellectual property protection, since we have incorporated some databases.

Q: What other challenges would you need to consider?

A: Our software currently faces many challenges. For instance, since our project is an integrated synthetic biology software, the errors generated in the algorithm simulation of each step may be amplified by the next step, leading to a large deviation in the final result. ThusNext, professors or companies in synthetic biology may not necessarily trust the predictions of our software. In addition, the algorithm is not optimized enough so the operation speed still needs improvingis not so fast. Last, those who are not skillful in synthetic biology don't necessarily understand the design of circuitpathways and retrieval functions. Faced with these challenges, we searched a large number of reviews and researches and optimized the algorithm to improve its operating efficiency. In terms of users’ interaction, we changed the description and the page to make our design more concise and humanized to lower the threshold of our project, so that users can use our software more quickly and conveniently.

The possible problems our software might have. The result shows that interviewees might have doubts about the prediction accuracy of our software, which may be a reason for not using our software.

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