Team:SYSU-Software/Contribution
Contribution
In order to understand the primary need of synthetic biologists, we sent out questionnaires to experimental teams and companies(see HP page https://2020.igem.org/Team:SYSU-Software/Human_Practices ). Receiving a large amount of feedbacks, we found that many members in these teams were troubled by the undesired experiment results, and some of them required for a specific searching platform. Primarily focusing on their needs, we designed Maloadis, hoping to become a competent assistant for synthetic biologists.
Standardization
To build a image searching platform integrated with circuit design, we need to obtain standardized forms of genetic circuits. To achieve this, we use picture recognition and machine learning techniques to extract parts and gene location relationships from various forms of genetic circuit pictures. We then transform them into standard SBOL forms, which can be edited on our designing platform. What’s more, we integrated iGEM Registry into our database. Every genetic circuit in our software will be coded and virtualized with SBOL, promoting the use of standardized genetic circuit forms.
Engineering principles
The structure of our software was based on the engineering workflow, DBTL(Design-Build-Test-Learn), encouraging users to apply engineering principles to their projects. The designing part can be achieved by the searching and functional circuits design parts of our software. Then, our simulation part can provide beforehand results for later experiments. Finally, we provide parameter optimization module, which can make full use of experiment results and then obtain suggestions for optimalization. Maloadis completes the whole circle of DBTL, which can be conducted several times in order to achieve the best results.
Human practice
We communicated with a wide range of stakeholders through questionnaires and meetings, understanding their needs and adjusting our software to them.
In order to enhance the collaboration between software teams and experiment teams, we participated in the ccic (Conference of China iGEMers Community) and hosted the ccic software workshop. We’ve received valuable advice from the judges. Through the communication with other software teams, we make sure that our projects are complementary to each other, focusing on different layers of synthetic biology. Because of the pandemic, the schedule of the experiment teams was left behind. Thus, our computational methods are quite necessary.
We believed that this kind of collaborations should be further promoted. With the cooperation of each team, we will be able to accelerate the development of synthetic biology.
Education
We host a seminar for students. These students are often not quite familiar with synthetic biology nor iGEM. We used vivid explanations and interesting examples to arose their interest towards synthetic biology and help them to have an idea of iGEM, which may encourage them to pursue the path of synthetic biology and participate in iGEM.(seen education page https://2020.igem.org/Team:SYSU-Software/Education )