There are many limitations to a software team working alone on the design of a project, so we collaborated with lots of teams this year. Though during the outbreak, it is difficult to conduct face-to-face exchanges, yet we have collaborated with many teams to troubleshoot a problem employing online communication.
Collaboration 1: Tongji_China
Since we are from the same school, it is more likely for us to develop integrated collaboration. This year Tongji_China designed a kind of engineered bacteria to effectively detect and diagnose the chronic lower gastrointestinal bleeding. Therefore, due to their project theme uninvolved with the metabolic pathway, it is so regretted that our software could not help them, and they could not test our software by searching for or simulating what they were concerned about, like the cooperation between us over the past few years. Even so, we can collaborate in some respects, like education.
Firstly, we did some educational work for high school students who are interested in the university's biological research. The Seeding Program is a characteristic enrollment program at Tongji University. With help from the school, we two teams co-hosted the program to introduce biology, synthetic biology, and iGEM to them, which can guide their choice of majors. On July 19th, 2020, we had an online meeting with about 40 high school students. We popularized the knowledge of iGEM and synthetic biology to them and showed some of our software project's functions. Last, we also answered the students' questions and collected some questionnaires and feedback about the results of the whole program. That was our first collaboration, and in the following months, we began to seek new shared objectives related to both of our projects.
figure1. Collaboration between Tongji_China in The Seeding Program
Collaboration 2: SYSU-Software
We contacted SYSU-Software after we saw the promotion video at South China Communication Conference. In some respects, our two projects were semblable, and it was much possible for us to overlapped with each other. From another point of view, it was also an excellent chance to collaborate, differentiate our projects, and refine them. Therefore, we had a conference online on June 13th, 2020, and comprehended deeply respective projects. At that time, the software of SYSU-Software also had the functions of pathway searching and metabolic simulation. We discussed and decided to differentiate our software's background and direction specifically, SYSU-Software focused more on the gene circuit and abandoned the metabolic database, and we emphasized the metabolism. It was unnecessary to change the similar models and methods used in our software, and some suggestions were made on these points. Our two teams have been in touch ever since and hope to promote further collaboration in complementing each other.
figure2. Collaboration between SYSU-Software
Collaboration 3: UESTC-software
The project of UESTC-software, CPD3DS, directly uses the structural domains as the basic unit to analyze protein structures. On August 9th, we contacted them to discuss the enzyme parameters which both our projects are involved with. Some enzyme parameters were used both in the pathway ranking of our project and analysis of classified protein domains in their project. On September 9th, we had a conference online to discuss how to optimize the enzyme parameters, such as Gibbs free energy. Because the pathways found by our software consist of various enzymes, there is an opportunity for us to collaborate in this field and to prepare for the future development of our projects.
figure3. Collaboration with UESTC-software online
Besides, we tried out their game and made some suggestions: the game is too difficult for non-biological students; In the 3D Lab, it would be of more popular science significance to add different domains with names and introductions. Then, we tested each other’s software and offered advice on design and use. They said that if there is a small example video on the top of the website, users can get used to this function faster, and they hope the search results provide more diversified presentation forms. We also proposed some font size suggestions and wished their software to give some functional descriptions on the NeuralStyle and Home web page.
figure4. Collaboration with UESTC-software online
Collaboration 4: SJTU-software
We met each other at the first Conference of China Software iGEMer Community (CCSiC) on August 15th. SJTU-software was ready to make a relatively convenient biology teaching and experiment auxiliary package, which may mitigate the non-face-to-face learning's inefficiencies due to the epidemic. On September 22nd, we held a seminar online to talk about the software's problems and put forward some advice for each team. Interested in the Virtual lab function of their project, we made an idea that was integrating our software into their Virtual lab so that teachers and students can use our software in their lab for teaching. Their software was still running in a single thread at that time, so it was too difficult to insert our software. We may try putting links directly in their Virtual lab. Besides, when their analysis of Orvza sativa L (rice) genome involved in metabolism, we can offer some help.
Collaboration 5: Workshop in CCiC
On August 30th, the Workshop held by iGEM software teams in China went smoothly. At the same time, we invited the iGEM experimental teams to participate in the Workshop to promote the communication and cooperation between the iGEM software team and the experimental team. In the first part of this Workshop, each software team made a presentation to demonstrate and introduce the project, respectively. In the communication section, we learned a lot about the experimental team's needs, and we discussed some exciting things when preparing for the competition. We hope each iGEM team can become more connected even during the epidemic.
figure5. Collaboration with software teams in Workshop