Overview

Our team conducted in-depth collaboration with SJTU-software in previous years. This year we continued the close relationship with them. We contacted them through social networking platform at the beginning of our project. Due to the impact of COVID-19, we were unable to communicate with their team members face to face, so we adopted many forms of communication as follow.

https://2020.igem.org/Team:SJTU-software/Partnership

Starting point of partnership

Since face-to-face communication is not possible, we communicate with all teams online. We have communicated with SJTU-software during the design phase of the project, and also had in-depth exchanges later on. We showed great interests to mutual project, and found that there are many areas for cooperation between our two teams. In this way, we started our journey of cooperation.

RICAID

Their project is about building a rice database to help scholars more easily select the genes they need.

CPD3DS

Our project is about the classification of Protein Domains in 3D Shape to design a standard set of protein bricks.

Innovative forms of communication

This year we can't communicate face to face like before. But this did not affect our communication. We used our free time to host online meetings, exchanged the latest developments with each other, and gave opinions on each other's projects. In addition, they sent a team member to our school as a representative. The offline approach allows us to exchange feelings about the competition and make more emotional connections rather than just project cooperation. This method made our relationship closer.

How we collaborate

On June 27th, we held our first online meeting. We first introduced our projects and got to know each other. They put forward the idea of building a rice database, but at the same time they wanted to do a lot of other work, such as molecular modeling, laboratory management tools, etc. Considering the impact of the event, we suggested that focusing on one content and doing it well are more better. After understanding our project introduction, they gave us some suggestions about the visualization of protein domains. So we started thinking about what form of visualization would work.

After the first communication, we have confirmed our intention of partnership. Between June 27th and July 7th, our two teams are preparing the promotion tools for the project. We determined to make a game about how to splice domains in 3D shapes which could help users understand protein structure. Our game is called Protein Brick made through Unity. What they want to model is a virtual simulation experiment made through Unreal.

On July 8th, we conducted the second online communication. We sent the games we made to each other and tried to give some suggestions. Regarding their games, we suggested that they could simplify some of the operating steps in virtual experiments, because too many operating steps easily made users feel bored. For our game interface, they thought the interface is a bit rudimentary, and they suggested making some beautifications. After this exchange, we have both made improvements.

From July 15th to July 25th, SJTU-software held a summer camp with the theme of synthetic biology at Huangchuan Middle School in Xining City, Qinghai Province. They let local students use their virtual laboratory. At the same time, they also showed the students Protein Brick game made by us. In the process of using our two games, the students learned a lot of biology related knowledge in an interesting way. In order to better improve our projects, we distributed questionnaires to students to collect their experience and suggestions on these two projects. Our third online communication took place on July 28th. In this exchange, SJTU-software introduced the results of their summer social time to us. In addition, our two teams also had an in-depth discussion on the algorithm. Since our game is relevant to our project core, their feedback about Protein Brick Game is very important to us. And also both of our teams have realized the establishment of the database in the project, and we have also used algorithms such as K-Means. After the exchange, we have a full understanding of the algorithm and laid the foundation for the subsequent analysis.

In order to better cooperate, SJTU-software sent one of their team members, Mu Junxi, to our school for offline communication. From August 6th to August 10th, Mu Junxi had full exchanges with us on this phase. In addition, Mu Junxi shared with us some of the difficulties and feelings their team encountered during the project. We showed him around our campus, which narrowed the distance between us.

Our fourth online communication took place on August 16th. In this exchange, we showed SJTU-software Probrick, a 3D-printed protein building block designed through visualization. They suggested that we could consider making it more interesting for users. And also, for their rice database, we suggested that they could add data for different objects.

On September 11th, SJTU-software have face-to-face communication with another team in their school. They also asked the biox team to comment on our project from the perspective of experimenters. They think that our CPD3DS(Classification of Protein Domains in 3D Shape) is very useful for experimenters.

On September 22nd, we had a long online meeting. We thought about ways to better integrate our projects. SJTU-software selected several representative genes in their rice gene database and found out the proteins they expressed. They gave these proteins to us and we analyzed these proteins' structure. In addition to this online communication, we invited them to watch our sign language video?Your Existence?. After watching our video, they all think this work is very meaningful. Our sign language video uploaded on Bilibili ( video link)

During the holiday period from October 1st to October 8th, our two teams were developing the project website. We invited each other to test the website and provided feedback every day. We constantly improve our web pages based on the suggestions made by the other party.