Earlier

3.20-4.5

We made posters and prepared a PPT for the iGEMer recruitment presentation. We recruited 19 students from different disciplinary backgrounds and different grades. We are passionate about iGEM, but the road ahead is also full of challenges.

4.8

We held the first meeting of all members and made an overall introduction to the whole process of iGEM. Each member also introduced themselves and explained their respective strengths to facilitate the subsequent division of labor arrangement. At the same time, the biology group started to research the project and formulate the topic.

4.8—4.22

Within two weeks, the biology group researched previous years' iGEM projects for inspiration and determined our initial idea: using computer knowledge to assist in solving biological problems. The biology group consulted with seniors to collect the difficulties they encountered, and under the leadership of Zhuofan Cui, we determined our initial topic: exploring the construction of a bioinformatics tool in order to achieve a one-stop service for protein stability optimization.

4.22

We held a second all-members meeting, where Zhuofan Cui introduced our preliminary program to all members and determined the next steps for the members of different groups. Students from the Biology group started to investigate bioinformatics tools. It was obvious that it was quite difficult to get so many students from different disciplinary backgrounds to work together to accomplish something, but we still believed that we could overcome the difficulties.

Late April

USTC-software participated in the Science and Technology Week organized by the University of Science and Technology of China (USTC), where we set up a booth on campus and talked about synthetic biology and helped children to complete some hands-on experiments. Primary and secondary school students from all over China visited our booth and showed great enthusiasm for synthetic biology.

5.10

We held the third meeting of all members, and unanimously approved Cui Zhuofan's proposal. The art team started to make the promotional posters and the project logo, the front-end team and the back-end team started to work together to learn the specific ways of calling the source website and to confirm their understanding, ready to start the writing work, and everyone in the team actively prepared for the work.

5.10-6.5

The front-end and back-end investigated the few software identified even further, analyzing SWISS-MODEL, PROSS, AlphaFold2, Jalview, PyMoL, PLIP, NovoPro, and Uniprot for their functionality, open-source status, ability to be deployed locally, and input/output feedback methods. The difficulty of the task was identified: the lack of specific ways of using these software and the trade-offs between the relevant output information.

6.5-7.16

The back-end team started investigating Zero-shot Learning, which includes both local and global evolutionary models.

Mid-term

7.16-7.25

The front-end team used the wiki source code to familiarize themselves with the GitLab development operation, understood the basic structure of the source code, learned how to refer to external libraries and images with the reminder of USTC-Software2022, and divided the tasks for each team member. The back-end team went a step further and tried to deploy open source code. In this process, we frequently encountered problems such as old code versions, incomplete code, and effects that did not meet the requirements. In the end, only the EVMutation and Multi-Sequence Comparison sections were successfully completed. After hitting the wall several times, we discussed the feasibility of the current solution with the biology group, and finally we decided to go back to the original solution.

7.16-8.5

After the midterm exams, we visited our PI, Mr. Hong Jiong, and explained to him our problem that it was difficult for the Biology group to work together with the front and back-end students because of the different knowledge backgrounds. Mr. Hong gave a lot of practical advice. After that, we decided to divide the whole team into several groups, each including two students from the biology group and two students from the back-end group, and each group was responsible for a portion of the research and development work, in order to promote the communication between students. Finally, our team functioned organically.

8.5-8.11

Students in the front-end group applied for our cloud server on the Tencent cloud platform, investigated how to use Flask to build our software website, and made a preliminary attempt to build the website. Students in the back-end group deployed the code to the cloud server and actively cooperated with the front-end group to debug the program.

8.18-9.6

We collaborated with iGEM-USTC to provide a duplex codon-based optimization algorithm for codon optimization. The back-end group has completed single codon optimization, and the back-end group tries to improve the performance of the existing single codon optimization with the duplex codon algorithm. Since there is no readily available data on the frequency of duplex codon distribution in different species, the back-end group, after consulting with iGEM-USTC and the biology group, wrote a script to count the distribution of duplex codons on the National Library of Medicine.

The front-end group designed and developed basic UI interfaces for each part of the software based on the research work of their respective groups, and began to try to develop the front-end and back-end interactions. In the process of interaction development, due to the lack of experience, there was a mismatch between the send destination address and the receive address in the message transmission. Under the guidance of the senior of USTC-Software2022, we gradually solved the problem and finally found and solved the problem, and realized the unification of the form upload function and the address based on the ajax tool.

9.1-9.12

The back-end team completed the testing of EVMutation multilocus mutation and created a mutation cloud based on the mutation results.

The art team successfully completed the production of the promotional video for Prot-DAP.

The front-end started to beautify the user interface of the software with the design participation of the art team. In the process of interface beautification, in the spirit of striving for excellence, the front-end team and the art team reached a consensus on the first draft of our software page design after many discussions and comparisons of different actual effect diagrams, and after many revisions.

9.7-9.16

The team organized and participated in the Science and Technology Week volunteer activities, as well as community volunteer activities, explaining synthetic biology to children and parents.

The front-end team carried out the deployment of the back-end code on the cloud server, realized the front-end and back-end interactive functions of protein search, multiple sequence comparison, structure prediction, and primer design, and verified the feasibility of its operation. Subsequently, the development of the output visualization page and articulation of the software began. In the process of development, the students of the front-end group had an in-depth and extensive communication with the biology group. During the exchanges, the front-end group gradually grasped the biological significance of the inputs and outputs of each part of the process and how they were connected, determined the format of the visual outputs of each part as well as the articulation hints, and also understood some of the shortcomings of the current website's design, added file uploading functions, and finally established a preliminary and usable website.

Later

9.18

Led by Mr. Desmond Hong, we visited Huaheng Bio-Research Institute and talked with the head of the research institute, who gave us a lot of meaningful suggestions.

9.23-10.13

We solved the algorithm problem of codon optimization and added the function of PSSM matrix construction to the software, and organically connected the software of each link. With user-friendliness as an important indicator, we further beautified the interface of our product by adding process advancing arrows and input prompts, adding a loading animation, providing check buttons for site mutation to directly modify the corresponding sites, and realizing the guidance of the whole process to make it more suitable for the public to use and more user-friendly.

We completed the content writing of the wiki according to the task assignment, and cooperated with the artist to beautify the wiki interface.

10.20

We completed the team's introductory video