Overview

The year of 2020 has witnessed how iGEM teams endeavored to collaborate with each other in the community despite the COVID19 pandemic. This summer, our team held the first Conference of China Software iGEMer Community (CCSiC), participated in the 7th CCiC (Conference of China iGEMer Community) and held a workshop with teams from many different tracks in China. During the process, Tongji-Software reached us and we started a season-long partnership. These collaborations gave us the chance to make friends with iGEM teams of all tracks and profoundly shaped our project.

Silver Collaborations

1. CCiC online:

A lot of software teams in China have participated in iGEM for many seasons, but there has not been any platform for us to have discussions on software development for synthetic biologists. Therefore, we decided to hold an online conference for all Software teams in China. On August 15th, we held the first Conference of China Software iGEMer Community (CCSiC). All software teams in Mainland China including SJTU-Software, Tongji-Software, USTC-Software and UESTC-Software were invited to participate in the activity. During the two-hour conference, all teams presented their project themes, design ideas, and discussed software applications in synthetic biology, as well as shared the strengths and weaknesses of each team's project and what they could collaborate with in the future. Our advisor Tianqin Li and Dr. Jianhua Yang also gave their advice on each team’s project. At last, we raised questions and made discussion with each team. We all learned a lot from CCSiC, and it also contributes to our further collaboration with Tongji-Software.

Here are details of CCSiC.

Part 1: Project Exhibition

The leader of SJTU-Software Ruiqi Lv introduced to us their project DIGIASST, which was convenient for biology teaching and laboratory assistant for assisting cloud laboratory teaching.

The leader of Tongji-Software Chunfu Xiao, showed us their metabolic pathway searching software Synthesis Navigator, a search engine software which combined a large number of databases and evaluated the pathway accuracy of searching results through a variety of algorithms.

Wang Bin, the leader of UESTC-Software, demonstrated their software that can classify and standardize protein domains. Their software had functional analysis of structural domains and guiding protein-related design.

Yulong Ming, the leader of USTC-Software, introduced to us their chain platform for protein molecular simulation, which can predict and simulate the affinity of proteins through algorithms.

Part 2: Comments and Q&A

Dr. Yang suggested that UESTC and USTC-Software, which both focused on proteins, can communicate with each other on collaborations and some algorithms. Advisor Tianqin Li shared his some recent advances in the field of protein interaction and algorithms such as Machine learning and some new databases. We also discussed the feasibility of our software and why we used the certain algorithm. And we also exchange our e-mail for further communication.

2. Workshop:

On August 30th, the Workshop of iGEM software teams in China were held by us. Compared with the CCSiC two weeks ago, each software team also improved and promoted their own project. At the same time, we invited the iGEM experimental team to participate in the workshop in order to promote the communication and cooperation between the iGEM software team and the experimental team.

In the first part of the workshop, each software team made a report video for 20 minutes, which was combined with PPT to demonstrate and introduce the project of the software team.

The second part is communication. First of all, we discussed whether the software team's project meets the needs of the experimental team. For example, in the design of the actual experimental project, whether the software is too simplified and whether the experimental team needs more detailed design, etc. At the same time, the experimental team also shared their current progress of the competition. Due to COVID-19, most of the experimental teams did not make much progress in the wet experiment, and they mainly stayed at the stage of searching for articles. Among them, the experimental idea of SYSU-China is about dsRNA directed evolution to obtain ADAR1 inhibitors. The experimental idea of OUC-China is a design of RNA switch and logic gate.

Finally, we talked about how the lab team might need help from the software team. The software team can provide the experimental team with technical support and help in data set after article searching, wiki production, video production, art design, etc. And we also exchanged contact information for future communication and collaboration.

3. Tongji-SYSU-Software:

This year, we collaborated with Tongji-Software throughout the whole season. We cohosted the CCSiC, and the workshop in CCiC. We have discussed our projects online together, troubleshot for each other and finally combined metabolic design and software design together. The following section, Partnership, we documented how our partnership shaped both of our projects.