"This year, our partners and us, have benefited a lot from partnership！"
At different stages and levels, we had in-depth conversations with both teams, XJTLU-CHINA and SJTU-Software, and we all achieved mutual benefits in the process of cooperation.
Benefited to the similar project contents of the both teams, we provided suggestions and help for each other's project in many aspects. You can click here for jump to XJTLU-CHINA.
Figure: XJTLU-CHINA & Tongji_Software
XJTLU ←→ Tongji
This year, we jointly set up a popular science website: xtphage.com (the domain name is the combination of the initial letters of 'XJTLU' and 'Tongji', and the word 'phage'). On this concise-layout website, we introduced synthetic biology, bacteriophages, drug-resistant bacteria and other concepts through interesting and engaging articles. In the process of building this web page, we used our front-end visualization skills to build it, while the two teams shared responsibility for updating articles for the content of the site.
Figure: Popular Science Webpage
People can also be navigated to this popular science page at the end of the small game made by Tongji_Software.
Figure: End-of-game screenshots
We all hope that through our publicity, more and more people could be engaged in iGEM and synthetic biology.
Mentor A team
XJTLU ←→ Tongji
The two teams met online for the first time on July 16th, 2021. In this meeting, both sides first gave a brief introduction to their own projects, and then listened to the suggestions from the other team. Both teams were inspired to some extent.
Figure: First online meeting with XJTLU-CHINA.
During the meeting, XJTLU-CHINA proposed that there was a problem with the phage supply of their team, and subsequent experiments could not be carried out. Then, after the meeting, to replenish their phages supply, we contacted many companies in Shanghai, such as Ruizhui, Tanpu, Albertson, etc. We did everything we can to find phage suppliers for them, and we were glad they finally get their phage source in time.
XJTLU ←→ Tongji
During our partnership, XJTLU-CHINA and us also cooperated in human practice. With the suggestion of XJTLU-CHINA, we made a questionnaire to investigate people's views on phage therapy. With the reminder of us, they learned about the annual China Superbug Infection and Phage Prevention Summit Forum and timely participated in the conference online.
Figure: Chinese Superbug Infection and Phage Prevention Summit Forum was live streamed online
XJTLU ← Tongji
The leaders of two teams, Xinyan Han and Yanping Zhao, make frequent communication on project progress. In the process of communication, we learned that they had doubts about the mathematical model, therefore on July 27th, 2021, in order to help them, we held an online meeting.
Figure: Online meeting with XJTLU-CHINA for supporting modeling
At the meeting, XJTLU-CHINA pointed out that the first half of their model, "determining the amount of protein released when a bacteriophage infects a bacterium," is questionable. After listening to XJTLU-CHINA, we provieded some suggestions for them:
1. Try to find bioinformatic tools or related literature in this field;
2. Based on the experimental results, try to carry out a curve fitting in order to finding the function.
At the end of the meeting, XJTLU-CHINA expressed their thanks to us for suggestions.
Figure: First half of XJTLU-CHINA's model
XJTLU → Tongji
Benefits from the similar theme of both teams, XJTLU-CHINA provided valuable experimental verification for our software: Phage-MAP. Phage-Map predicted a score of 0.995 for the combination of T4 phage and E.coli.
Figure: Phage T4-E.coil pair in the Phage-MAP
However, this prediction, could not be verified by ourseleves. Fortunately, XJTLU-CHINA has the relevant experimental materials. By conducting plaque assay, they confirmed that T4 phage can crack E.coli in reality, proved the accuracy of our predictions
Figure: Phage plaques formed by Phage T4 in the E.coli
Thanks to the similarities between the projects of XJTLU-CHINA and us, we put forward many valuable suggestions for each other and provided certain help for each other's projects in many aspects and dimensions.
Through the Chinese iGEMer chatting group, we got contact with the leader Yuanjie Hu of SJTU-Software on April 20th. This year, the topic of their project is DNA computing. They did so much work that their project was fantastic. Although themes of our projects differ widely, we still have helped each other in many aspects since April 2021, because of our similar role as software teams and similar background in biological and computer. You can click here for jump to SJTU-Software.
Figure: SJTU-Software & Tongji_Software
April - May
SJTU ←→ Tongji
Two teams got in touch in April. During this period, the leaders of the two teams exchanged their brainstorming idea through WeChat from time to time. The main topic was focused on how software teams help synthetic biologists and iGEMers overcome some obstacles.
It is worth mentioning that we proposed "want to design a software to assist the design of Toehold-RNA-Switch" during a brainstorming session. Although the we did not carry out this project, we still had accumulated related knowledge which involves the prediction of RNA secondary structure when investigating this idea. This knowledge laid foundation for the subsequent exchanges between the two teams.
In addition, thanks to the fact that both teams are located in Shanghai, the leaders of the two teams, Yuanjie Hu and Yanping Zhao, successfully met offline for the first time on May.
SJTU ←→ Tongji
At that time, the project themes of the two teams have been determined. Through wechat group exchanges, the two teams had a preliminary exchange on respective backgrounds, research value and computing technique of respective project. During the online meeting, SJTU-Software mentioned the idea of building a DNA computing platform to assist in early cancer screening, mainly related to secondary structure prediction. Based on what we know, we recommended a software "NUPACK" for RNA secondary structure prediction to them, and they suggested us try to obtain useful information from other teams focusing on intestinal flora or phage.
SJTU ← Tongji
During this period, SJTU-Software mentioned that their prediction of RNA secondary structure did not perform well. After learning the whole process of their project through online meeting, we discovered that they used the "One-Hot" method when encoding nucleic acid sequence information. However, we pointed out that the sparse matrix obtained by "One-Hot" encoding has the problem of high dimension, isolated and irrelevant words, and poorly semantic information representation.
Figure: Example of One-Hot encoding of the DNA sequence "TTTGACTCGT"
After we informed them of this view, SJTU-Software did further research on encoding method and eventually changed the encoding method from "One-Hot" to the current "Word2Vector".
Figure: Communicated with SJTU-Software
A team member of SJTU once said, "Tongji Software's suggestions have paved a new way for us. That has further improved the accuracy of our prediction results. Anyway, I am very grateful to them for their valuable suggestions."
SJTU → Tongji
On August 7, two teams communicated offline. During the process, our team proposed that the Spacer_based_BLAST method has high accuracy and low detection rate. With the exact communication, SJTU-Software put forward valuable opinions to us. They thought that "now that the detection rate of alignment method is too low, why not try non-comparison method". With their suggestion and later literature research, we decided to add an alignment-free evaluation section, which plays a crucial role in our complete project model.
Figure: Conmmunicated with SJTU_Software on August 7th
SJTU ←→ Tongji
At the CCiC meeting, our two teams communicated offline again. In this process, we pointed out that the presentation of SJTU-Software was too professional to understand. Taking our suggestion, SJTU-Software made improvements in project sharing and project display to make it easier for the audience to understand. In addition, the two teams exchanged views on Education, Engineering and other areas. Through this communication, we had a clearer understanding of these areas. After viewing our work of Communication, SJTU-Software was encouraged by us to set up popular science web pages and make popular science mini-games.
Figure: Two teams at CCiC Conference
September - Octorber
SJTU ←→ Tongji
Considering the deadline of Wiki freeze, we did not hold meetings, but we still occasionally communicated via WeChat. During this period, we shared some resources with each other, such as Wiki design knowledge, artistic material website, etc.
Since the first contact with STJU-Software in April, we have been communicating throughout the season. During this period, the communication between us not only stayed at the point of sharing resources with each other, but also we all exerted a clear understanding of each other's project. Also, we both teams made improvements on the projects by taking the advices of the other team.
All in all, we are very grateful for this international competition organized by iGEM, which not only allowed the two teams to make acquaintances with each other, but also allowed the members of the two teams to gain such valuable friendship.
★ Ending Words
Cooperation is such a valuable thing to do. We are sincerely grateful to our partners for their help and advice!