Team:SYSU-Software/Partnership
Overview
This year, we collaborate with Tongji-Software throughout the whole season. Despite the COVID-19 epidemic, we found a way to work closely to each other through online meetings and conferences. Our partnership has shaped our project in a fundamental and profound way.
Early stage — conferences and workshop
After collaborating for a period of time online, we manage to exploit the use of online meeting platforms, and realize that this special period time of COVID-19 actually give us a chance to find ways to cooperate with teams far away.
Inspired by this new collaboration pattern, both of our teams want to take this to a broader level. On August 15, our team held the first Conference of China Software iGEMer Community (CCSiC). Tongji-Software assisted us to successfully organize this event and participate actively in all sessions.
Our introduction video uploaded on SZU-China's Wechat official account (szuigem)
Our introduction video uploaded on bilibili (video link: https://www.bilibili.com/video/BV11z4y197xe)
Tongji-Software reached us because they discovered the similarities between our projects. On one hand, we were worried whether the overlapping goals will diminish our uniqueness. On the other hand, we saw possibilities in collaboration. We arranged our first online meetings using the app Tencent Meeting on June 13, 2020.
Online meeting with Tongji-Software on June 13, 2020, Tencent Meeting
After discussions, we had a deeper understanding of each other's project. The following table shows our discussion results:
| similarities | differences | ||
|---|---|---|---|
| • We both aim to create a software that help synthetic biologists design • Both of our software designs feature search engine and simulation |
• Tongji-Software focuses on metabolic pathways and Metabolism Simulation • Our team focus more on genetic circuit design and gene expression simulation |
||
| How to collaborate: Metabolic engineering and genetic circuit engineering are both important in synthetic biology. We can combine metabolic pathway design and genetic circuit design together and build an integrated design platform. | |||
At first our team decided to incorporate FBA in our software design, and Tongji-Software also want to use FVA and FBA in the Metabolism Simulation, but after discussion with them, we decided to focus only on genetic circuit design or metabolism separately, so that we can provide users with better experience and more complete workflow on both aspects.
Beginning stage — design idea inspiration
After collaborating for a period of time online, we manage to exploit the use of online meeting platforms, and realize that this special period time of COVID-19 actually give us a chance to find ways to cooperate with teams far away.
Inspired by this new collaboration pattern, both of our teams want to take this to a broader level. On August 15, our team held the first Conference of China Software iGEMer Community (CCSiC). Tongji-Software assisted us to successfully organize this event and participate actively in all sessions.
CCSiC online meeting
Tongji-Software and SYUSU-Software presentation on CCSiC
Software designers need to investigate potential user demand, which means we need to connect to teams from all tracks. On August 30, our team held a workshop featuring Optimization of System Construction Process during Conference of China iGEMers Community (CCiC). Tongji-Software co-hosted the conference with us. During the conference, together we inquired about software needs, and answered questions on algorithms and models.
CCiC workshop
After the conference and workshop, our team realized that to facilitate synthetic biology development in the future, algorithms enabling researchers to complete complicated designs in a more efficient manner is in need. Therefore, we set up another project goal -- design automation. And Tongji-Software continued to develop the metabolic functions, such as how to optimize and simplify the form of the results.
3.Middle stage — incorporation of genetic circuit design and metabolic design
In early October, Tongji-Software and out team have finished most of our software design. We continued exchanging ideas online throughout the whole season. On October 4, we arranged another meeting discussing how to combine metabolic design and genetic circuit design together.
10.4 meeting with Tongji-Software on Tencent Meeting
This meeting was decisive for our collaboration. We combined our workflow together as the following graph:
Workflow of our combined softwares
In both of our software, users can find links to the other team's wiki project page and have easy access to metabolic engineering and genetic circuit design within a consistent workflow.
In our software, user will see a pop-up window which briefly describes Tongji-Software's Synthesis Navigator.
The blue pop-up window up right in the above picture is a brief description of Tongji-Software's Synthesis Navigator.
Click "learn more", and users will be linked to a page describing the function of Synthesis Navigator.
Click "visit their website" and users will be linked to https://www.tjigem.com/ to start using Synthesis Navigator.
When using Tonji-Software's Synthesis Navigator on https://www.tjigem.com/ , users can find the link to our software Maloadis in the second function Pathway Finder (https://www.tjigem.com/pf).
Click "Maloadis" in blue and users will be linked to https://maloadis.sysu-software.com to start using Malodis.
Check our demonstration video and Tongji-Software's demonstration for more details
https://2020.igem.org/Team:Tongji_Software/Proof_Of_Concept.
4.Late stage—test & troubleshoot
We tested Tongji-Software's Synthesis Navigator and gave them comments. Check herefor further details.
Chunfu Xiao from Tongji-Software gave us comments and advice after using Maloadis. In general, he thinks our software is a very powerful tool for synthetic biologist. He gave us suggestions on:
• Incorporating key-word search and fuzzy search in our software.
• The design canvas takes up too much of the screen, drawing user' s attention away from our fucntions.
We attach great importance to feedback from iGEM teams. Tongji-Software's advice will be our direction in the future and we will keep improving our software.
