Team:Tongji Software/Partnership



Partnership 1: Tongji_China

    Because Tongji_China's project is not involved with metabolic pathways, it is relatively hard for us to provide help for them in pathway retrieval and validate our software. We had conferences several times and discussed other matters such as modeling, cooperation in science promotion activities, and publishing popular science articles.
    Firstly, On July 19th, 2020, with the school's help, we two teams co-hosted the Seeding Program online to introduce synthetic biology, iGEM, and our projects to about 40 high school students, which can be a guidance for their choice of majors. Last, we answered the students' questions and collected some questionnaires and feedback about the results of the whole program. More details in Collaboration. After that, we continued our cooperation.

figure1.Collaboration online between Tongji_China in The Seeding Program
figure2.Collaboration online between Tongji_China in The Seeding Program
figure1&2. Collaboration online between Tongji_China in The Seeding Program.

    Then, because our software team members are good at modeling, we had conferences together about the method of modeling used by Tongji_China and some daily events during the game. Tongji_China used three models to determine the route of administration, coating materials of drugs, the start time of the test, and to predict the location of the bleeding point. We discussed their model's hypothetical environment and the scenarios where their treatment used, for instance, whether the fasting environment in their first model needs patients to wait a few hours after a meal before taking the medication.

figure3.Collaboration between Tongji_China in modeling
figure3. Collaboration between Tongji_China in modeling.

    At other times, we two teams were in the operation of a WeChat Official Accounts publishing some popular science articles. The original intention of this promotion platform is to let more students know about IGEM and synthetic biology. In these months, we recorded some science promotion activities, and some popular science articles about engineered probiotics, synthetic biology medicines, metabolism and metabolic engineering were published widely. It is great feedback that more than several thousand people have read our articles.

figure4.Collaboration between Tongji_China in WeChat Official Accounts
figure4. Collaboration between Tongji_China in WeChat Official Accounts.

    Last, with the help of Tongji Innovation Club of Life Science, we did a science promotion activity for biology students together on October 13th, 2020. We popularized the knowledge of iGEM and synthetic biology to them and also introduced our two projects. The response was excellent, and many students began to be interested in the IGEM competition.

figure5.Collaboration between Tongji_China in the science promotion activity
figure5. Collaboration between Tongji_China in the science promotion activity.

Partnership 2: SYSU-Software

    This year, we also collaborate with SYSU-Software throughout the whole season. We contacted them through mail 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.

1. Early stage: Inspired by each other

    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, and SYSU-Software focused more on the gene circuit and gene expression simulation, and we emphasized the metabolism pathways and Metabolism Simulation. It was unnecessary to change the similar models and methods used in our software, and some suggestions were made on these points.
    We can combine metabolic pathway design and genetic circuit design together and build an integrated design platform. Our two teams have been in touch ever since and hope to promote further collaboration in complementing each other.

figure6.Collaboration with SYSU-Software in CCSiC
figure6. The first conference with SYSU-Software

2. Mid-term: CCSiC and CCiC workshop

    We assisted SYSU-Software to successfully organize the first Conference of China Software iGEMer Community (CCSiC) and participate actively in all sessions. We watched other's presentations and found two teams both referred to the proposal discussed earlier, and the projects became more specific and completed. Both teams are moving in the right direction.

figure6.Collaboration with SYSU-Software in CCSiC
figure6.Collaboration with SYSU-Software in CCSiC
figure7&8. Collaboration with SYSU-Software in CCSiC.

    During the CCiC, we watched each other's presentations and posters again. Then SYSU-Software proposed to hold a workshop for the software team and strengthen our cooperation with the experimental teams. So, we co-hosted the conference with them and the successful completion of the activity enabled our two teams to have a deeper understanding and cooperation. Thereupon we began to look for a collaboration that combines the two software by the upstream and downstream approach.

figure9. Collaboration with SYSU-Software in Workshop
figure8. Collaboration with SYSU-Software in Workshop.

3. Late stage: Functional integration and testing

        Later we had a conference online and learned about the progress of each project on October 4th. SYSU-Software abandoned the metabolic database and established a database of documented parts, gene pathways, and prokaryotic transcriptional regulation. Then we have come up with some results:
         1. After users use our software and hope to change the expression of enzymes in pathways found by our software, their software can be used to design some functional switches or topology circuits as a result that our project is upstream of their project.
        2. When users use their software and pay attention to certain substances and reactions, our software can provide some enzyme information and related reactions, which indicates that our project is downstream of theirs.
figure9. Workflows integration.
figure10. Workflows integration.

        3. In order to achieve the above cooperation, we can leave links to each other's software in our software front-end or wiki to guide users. Click our software and SYSU-Software’s software for more details.

figure10. Collaboration with SYSU-Software online
figure11. Collaboration with SYSU-Software online.

figure10. Collaboration with SYSU-Software online
figure12. Our software link on Maloadis

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