Team:Tongji Software/Human Practices
Human Practices
1. Very Beginning
1.1. Background survey & Original idea
When we had only a preliminary idea, we used questionnaires to investigate the needs for the pathway-searching tool in a total of 14 teams that participated in the iGEM competition in 2019 or will participate in the iGEM competition in 2020. At the same time, We also investigated how these 14 teams were affected by the epidemic of COVID-19. We found that most of these teams need to design a pathway in their project, and most of them have a demand for a pathway-searching tool. Besides, this year's epidemic has intensified their demand for excellent pathway-searching software. Therefore, we have the idea of developing an integrated pathway design platform.
Besides, we counted the projects of 40 teams that participated in iGEM in 2018 and 2019. We found that 22 of the 40 teams' projects involved the design of metabolic pathways or gene circuits. In these 22 teams, 12 of their projects involved the design of metabolic pathways; the other 10 teams only involved the design of genetic circuits. Such statistical results have strengthened our determination to develop an integrated pathway design platform. On this basis, we completed the function of metabolic simulation and promoted the integration of the project.
1.2. An important revision of our idea
At the very beginning of our project, we communicated with Professor Changsheng Du and asked for some advice on our program. Before this communication, we have thought about using our software to create detailed protocols on the pathways found by the software. Prof.Du and his team have been working in the field of molecular biology for many years. After we told our ideas to professor Du, he said to us that although users can use the algorithm to find out the best plasmid for molecular cloning from the database, users' lab may not have ways to get the specifically recommended plasmid built by other labs. Additionally, the experiment condition will be more intricate than what a computer could simulate, so the recommended protocols would not reach some effective results. Accepting his suggestions, we finally rejected the function of protocol making.
figure1. The part results of questionnaires
Besides, we counted the projects of 40 teams that participated in iGEM in 2018 and 2019. We found that 22 of the 40 teams' projects involved the design of metabolic pathways or gene circuits. In these 22 teams, 12 of their projects involved the design of metabolic pathways; the other 10 teams only involved the design of genetic circuits. Such statistical results have strengthened our determination to develop an integrated pathway design platform. On this basis, we completed the function of metabolic simulation and promoted the integration of the project.
figure2. Result of statistics
Summary: Through questionnaire surveys and statistics of the iGEM teams, we found that many iGEM teams need excellent pathway-searching software. Therefore, we have decided on developing an integrated pathway design platform, which can realize the function of pathway-searching and metabolic simulation.1.2. An important revision of our idea
At the very beginning of our project, we communicated with Professor Changsheng Du and asked for some advice on our program. Before this communication, we have thought about using our software to create detailed protocols on the pathways found by the software. Prof.Du and his team have been working in the field of molecular biology for many years. After we told our ideas to professor Du, he said to us that although users can use the algorithm to find out the best plasmid for molecular cloning from the database, users' lab may not have ways to get the specifically recommended plasmid built by other labs. Additionally, the experiment condition will be more intricate than what a computer could simulate, so the recommended protocols would not reach some effective results. Accepting his suggestions, we finally rejected the function of protocol making.
figure3. Communication whit Prof.DU
Summary: The function of making detailed protocols may not be of much use, so we finally rejected protocol-making function.
2. Mid-term
2.1. Cooperation with two student research teams
After we created the pathway design platform prototype, we cooperated with two student research teams from Xi'an Jiaotong-Liverpool University and Nanjing Agricultural University, which may be potential iGEM teams in the future. We handed over the prototype of an pathway design platform to these two teams and got some valuable feedback:
- In the pathways searched by the prototype, there may be intermediate products that are toxic to cells, so cytotoxicity should be considered when searching for the pathways. - The results of the prototype will be more intuitively displayed with the common name of the compounds.
We are very grateful to these two teams for providing us with such valuable suggestions. We accepted their recommendations and continued to optimize the pathway-search function in our software.
After we created the pathway design platform prototype, we cooperated with two student research teams from Xi'an Jiaotong-Liverpool University and Nanjing Agricultural University, which may be potential iGEM teams in the future. We handed over the prototype of an pathway design platform to these two teams and got some valuable feedback:
- In the pathways searched by the prototype, there may be intermediate products that are toxic to cells, so cytotoxicity should be considered when searching for the pathways. - The results of the prototype will be more intuitively displayed with the common name of the compounds.
We are very grateful to these two teams for providing us with such valuable suggestions. We accepted their recommendations and continued to optimize the pathway-search function in our software.
figure4. Feedback from a student research team
Summary: We have received great feedback from this cooperation, reminding us that we should pay attention to the cytotoxicity of intermediate products and the user-friendliness of the software 2.2. Conference of China Software iGEMer Community We participated in the first Conference of China Software iGEMer Community(CCSiC) online during the course of the project. This meeting was organized by SYSU-Software. A total of 5 software teams participated. In this meeting, we received suggestions and comments from some professors and other team members. What's impressive is that the professors and many other team members who participated in the conference were very interested in the function of metabolic simulation in our software and suggested that we develop this function deeply. Also, they gave us some advice on technical issues. We are happy to accept these suggestions and begin to focus on the development of metabolic simulation functions.
figure5. The first Conference of China Software iGEMer Community
Summary: During the first Conference of China Software iGEMer Community (CCSiC), we received some valuable suggestions on the function of metabolic simulation that make us pay more attention to improving this function. 2.3. the 7th Conference of China iGEMer Community Conference of China iGEMer Community, is an essential and helpful platform for iGEMers in China. We took part in CCiC from August 28th to 31st as one of all sixty teams. We introduced our project, our idea, and many experts in synthetic biology evaluated the software. We have received many suggestions from other groups and judges, as well as opportunities to cooperate with other teams. During CCiC, we received some suggestions on how to promote our software. Some judges suggested that we need to improve our software continuously, and we can try to cooperate with some scientific research teams later by using the software in actual scientific research or production. We think this is a good suggestion. In the subsequent progress, we also tried to cooperate with the scientific research team. Of course, this needs to be done for a long time, and it cannot be fully demonstrated in this year's iGEM. In addition, we also displayed our poster in CCiC and received some suggestions on how to improve our poster, which is very useful for our future poster production. At that time, in order to show more content in our poster, we wrote a lot of text. Judges gave us some suggestions on reduceing the text to make it more beautiful and express enough content at the same time.
figure6. the 7th Conference of China iGEMer Community
Summary: During CCiC, we were suggested to cooperate with the scientific research team to improve our software and promote it continuously. We are pleased to accept this suggestion and try to communicate with the scientific research team later. Besides, we have received some suggestions for the poster, which are also very useful.
3. Test & Future
3.1. Cooperation with a scientific research team
After completing the software's primary functions, we communicated with Professor Li Ping of Tongji University, introduced our software to her laboratory, and invited them to use it. We have received some feedback. Graduate students said that our software could effectively help their design and achieve the results they expected. Specially, we are grateful to Feng Junchen, a doctoral student in the laboratory of Professor Li Ping, who provided us with rich feedback after using it. He gave us much inspiration on how to improve this software can in the future. In the software he used, the pathway-searching function can only realize a one-step reverse search when the user only knows the target product. He thinks this function is very useful and suggested that we can improve this function. Now, our software can achieve a four-step reverse search when only the target product is available, allowing users to choose the pathway. When it comes to the function of metabolic simulation, he suggested that we display more compounds in the results, and prioritize the compounds that users care about. This is very enlightening, and we immediately try to realize this function. Now, our software allows the user to submit the compounds he cares about and can display more compounds which may change in the reactions.
All in all, we started by solving the problem of pathway design and tried to develop a piece of software that can be convenient for researchers. Through the integrated human practices among teachers, iGEM teams, and research teams, we optimized our software continuously and finally realized powerful, practical, credible, beautiful, and user-friendly software.
After completing the software's primary functions, we communicated with Professor Li Ping of Tongji University, introduced our software to her laboratory, and invited them to use it. We have received some feedback. Graduate students said that our software could effectively help their design and achieve the results they expected. Specially, we are grateful to Feng Junchen, a doctoral student in the laboratory of Professor Li Ping, who provided us with rich feedback after using it. He gave us much inspiration on how to improve this software can in the future. In the software he used, the pathway-searching function can only realize a one-step reverse search when the user only knows the target product. He thinks this function is very useful and suggested that we can improve this function. Now, our software can achieve a four-step reverse search when only the target product is available, allowing users to choose the pathway. When it comes to the function of metabolic simulation, he suggested that we display more compounds in the results, and prioritize the compounds that users care about. This is very enlightening, and we immediately try to realize this function. Now, our software allows the user to submit the compounds he cares about and can display more compounds which may change in the reactions.
figure7. Communication with Feng Junchen
Summary: The cooperation with the scientific research team has given us wealthy feedback and discovered many details for further optimization. We got some suggestions on reverse pathway-searching function and metabolic simulation, accepted these suggestions, and optimized our software. Now, our software can provide better results of the reverse pathway-searching and metabolic simulation. We think that cooperation with our target users like the scientific research team is precious and can help us optimize the software very well.All in all, we started by solving the problem of pathway design and tried to develop a piece of software that can be convenient for researchers. Through the integrated human practices among teachers, iGEM teams, and research teams, we optimized our software continuously and finally realized powerful, practical, credible, beautiful, and user-friendly software.