Team:Tongji Software/Attributions

Tongji Software | Pathlab

PROJECT
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TEAM

Group Photo

Here we are! Group photo of Tongji_Software!

TEAM MEMBERS



STUDENT



Bo Xu

Bo Xu

I am leader of Tongji_Software. My responsibility is to control the time line of project, organize each part together to complete our project. And I also be responsible for web front end work. For me, it’s a challenge to lead a team to attend iGEM, because this is the first time that attend competition. So, I tried my best to complete every part all the time. I’m glad to join in Tongji_Software, to prepare for iGEM. What’s more, I hope that each team member can get what they want here. Thanks for all of them, there will be gains when you pay.



Huili Shi

Huili Shi

I’m the team leader of Tongji_Software, Shi Huili. My main duty is the writing part and presentation, which means I should have a clear mind about the whole project frame. And as a team leader, I keep in pace of how every part is going on in order to make every part to meet the original expectations and know problems timely to adjust our plan. Taking part in iGEM is an opportunity to challenge myself, not only from the technical point of view, in this competition, I leant how to cooperate with my team members, how to collaborate with other teams, and how to get suggestions from professors and companies. It's the promotion of comprehensive quality, and I'm so proud to become one of the iGEMers.



Feiyang Xing

Feiyang Xing


I am responsible for modeling and algorithm implementation and Optimization in the project. In order to improve my code ability, I joined the team and met professional and creative teammates. The speed of our software operation increased gradually, meanwhile my algorithm and data analysis capabilities have also made considerable progress. I wish that our project will be gradually enriched in the future and will help the development of synthetic biology.



Zhaoyang Liu

Zhaoyang Liu


I am Zhaoyang liu from Tongji University, as a member of Tongji_Software my main job is coding and data collecting. I have done the part of data crawling, codon optimization, literature analysis, word cloud visualization, parts browser and some other things. Maybe I do not play an important role in this iGEM competition I am still a part of the team, not only for me but for all of us, we are all indispensable parts of our team. The feeling of behaving like a team is the most interesting and valuable experience that I have got from this iGEM journey. That is an amazing thing that a group of strangers at first can finally work on one project and even become friends.



Xue Piao

Xue Piao


I 'm Piao Xue, a member of Tongji software team, from Tongji university, China, majoring in software engineering. In our project, Pathlab, my contribution is to participate in the completion of the html pages and the interaction with the backstage of the software platform. As a student whose major is software engineering, honored to obtain the chance of participating in iGEM is definitely a precious experience to learn about new knowledge in a different field for me. It is amazing to imagine the exhibition composing of different disciplines. And I really expect this jamboree concerned about synthesis biology in late October this year.



Yao Nie

Yao Nie


I'm Nie Yao, mainly involved in model building and wiki making. I am very grateful to iGEM for providing me with a platform for engaging in synthetic biology. In the process, I was able to understand how my profession, such as programming, data structure and algorithm design, works in other areas. Also, this experience improves my abilities about data-dealing and team-working, and meet many like-minded people.



Zexin Zhao

Zexin Zhao


Here is Zexin Zhao, a senior student of Tongji University in China, who are interested in synthetic biology. In the team Tongji_Software, I am mainly responsible for theme discussion and writing. In the process of participating in the iGEM project,pathlab, I have experienced efficient group cooperation, made good friends, broadened my horizon and gained a lot.



Shudi Xu

Shudi Xu


I am responsible for the meeting records and finishing work of the whole project from the establishment, participate in human practice, responsible for external collaboration, writing and layout of the education part, and filling and supplementing the wiki page. I am very fortunate to witness our project – pathlab being built step by step from the very beginning. Our team is more like a small company, each of whom has its own role, but at the same time everyone is paying close attention to the work of other members. We all hope to achieve a good result, but the most important thing is to let me know the true meaning of cooperation, and everyone should do their best in the position they are best at.



Yuqiao Zheng

Yuqiao Zheng


From the Environment Design of D&I, Tongji university. I had received professional training of art, prefer science, do not adhere to the development of a single discipline. It is committed to the combination of science and art, in the constant search for the balance between technology and fine arts, the interdisciplinary practice of exploration. Our team is very creative and its members are very responsible. Fortunately, Tongji Software cooperated with me to build a WIKI, design the main vision and framework, and take charge of the main visual production and typesetting of poster.



Chenyan Liu

Chenyan Liu


My main job in the team is visual and communication design. I am responsible for the production of our group logos, cultural shirts and final presentation slides, posters. In this process, I deeply felt the cooperation between students with different major backgrounds. We also inevitably encounter problems such as unsatisfactory communication, but we all try our best to constantly understand each other and finally complete the work of each of us. Everyone uses their own expertise for the same goal.



Xiaotong Hou

Xiaotong Hou


I major in biotechnology, so it's really a big challenge for me to join in the software track. I'm mainly responsible for financial management, human practice and public relationship in our team. It's a fabulous experience for me to participate in iGEM, where I can make new friends and broaden my horizon.



ADVISOR



Wei Cao

Wei Cao


Team members of Tongji-Software are of great enthusiasm and talents in computer engineering and biology. It’s exciting for me to give suggestions and see how the program improved so well.



INSTRUCTOR



Jian Fei

Professor Jian Fei | Primary PI


IGEM is a great project. Its participants are a group of young people with little experience, so they dare to try difficult goals and are imaginative. This is its most attractive place, and you will always be surprised by their creativity.



Jiayu Chen

Professor Jiayu Chen | Secondary PI


Enjoy life, enjoy science, enjoy IGEM



ATTRIBUTIONS





Our software is divided into three functions: path search, enzyme selection, and parts browser. For the function of pathway search, we inherite the idea and infrastructure of last year's project, improve the algorithm, build a new model and expand the database. For the other two functions, enzyme selection and parts browser, these are the new sections added to our team this year. The function of the enzyme selection is completely completed by our team, as well as the parts browser uses UESTC_Software's database in the form of collaboration.




Team Member Attributions




Our team members have different professional backgrounds, so we have a reasonable division of labor and cooperation throughout the project to ensure that each member can play their own strengths and build an excellent software.


Bo Xu Huili Shi Xue Piao Feiyang Xing Zhaoyang Liu Yao Nie Zexin Zhao Shudi Xu Yuqiao Zheng Chenyan Liu Xiaotong Hou
Literature Research ✔︎ ✔︎ ✔︎ ✔︎ ✔︎ ✔︎ ✔︎ ✔︎ ✔︎
Thematic Discussion ✔︎ ✔︎ ✔︎ ✔︎ ✔︎ ✔︎ ✔︎ ✔︎
Data Acquisition ✔︎ ✔︎ ✔︎
Ranking Criteria ✔︎ ✔︎ ✔︎ ✔︎ ✔︎ ✔︎ ✔︎
Algorithm Implementation ✔︎
Coding ✔︎ ✔︎ ✔︎ ✔︎ ✔︎ ✔︎
Modeling ✔︎
Education ✔︎ ✔︎ ✔︎ ✔︎
Written Material ✔︎ ✔︎ ✔︎ ✔︎
Conference Records ✔︎ ✔︎
Design ︎✔︎ ✔︎ ✔︎
Human Practices ✔︎ ✔︎ ✔︎ ✔︎ ✔︎ ✔︎ ✔︎ ✔︎ ✔︎ ✔︎ ✔︎
Finance ✔︎

Table1. Team member attributions





Literature Research By searching and reading literatures, provide scientific basis for the realization of software functions.
Thematic Discussion Determine the direction of the project, that is, the functions that software can achieve.
Data Acquisition Collect data from different databases and organize them into the required format.
Ranking Criteria Set criteria for scoring and ranking the results (pathways and enzymes) of preliminary search in order to present the best results in the end.
Algorithm Implementation Improve former algorithm.
Coding Code all codes for the software.
Modeling When setting the ranking criteria and analyzing the results of the questionnaire, build and use a model.
Education Make small games to illustrate the process of building pathways step by step. Introduce iGEM to high school students
Written Material Prepare Wiki pages and contents for poster, contribute to presentations for communication, and organize the harvest of human practices
Conference Records Record the contents of each meeting.
Design Design Wiki pages, poster and software interface.
Human Practices Communicate with commercial companies and other school laboratories and provide continuous feedback
Finance Financial management

Table2. Attributions in detail








Professor Attributions




Professor Fei Jian, Tongji University

He gave us suggestions from the perspective of the use of scientific research, for example, the users can input one substance, and the user can see that what kind of products they can get through limited steps. This will be more illuminating in the early days of the project.


Professor Leng Ye, Tongji University

She let professors from the school of biology and science listen to the introduction of our project and gave us suggestions from the perspective of the use of scientific research. And she helped us to contact high schools in order that we can make presentations to high school students.


Professor Zhang Xu, ECUST

He gave us suggestions from the perspective of the organisms, the considered aspects of enzymes and the use of scientific research. For example, compared with making all enzymes into one single bacterium, making the flora seems to be more practical and feasible, meanwhile, we should take the influence of the external environment and cofactors into consideration.








Company Attributions




Genewiz

They gave us suggestions from the perspective of practical production. They pointed out the limitation of our reaction database and told us there might be some sequences can’t be synthesized easily in production.


GeneScript

We consulted them about whether there were any trials can verify what we were doing or whether customers do have the requirement of the arrangement sequence of enzymes. And we found that the combination sequence of enzymes can influence the efficiency of production and it’s really necessary to find an arrangement of enzymes which performs the most efficiently.








Other Team Attributions




Tongji_China

They gave us suggestions like cutting off useless results. And they give us many ideas of software visualization.


SJTU_Software

They told us that we have some disadvantages of login function.


UESTC_Software

They shared with us with the data they have collated of parts from the iGEM parts database and help us to test the website of our software.

PROJECT - COLLRBORATION

The paths found by our software are based on databases and algorithms, which need to be verified by practical experiments. At the same time, the results obtained by our software can provide support for the path design of the experimental team.


Through CCiC, we had a deep communication with three other experimental teams related to pathways construction. We know the substrates they own and the products they want to get,then try to design parts through Pathlab search paths and verify the pathways they implement.

COLLABORATION 1:TONGJI_CHINA

Since we are from the same school, Tongji_China and we have more integrated collaboration from the very beginning. We had conferences together for several times, and their project is about manufacturing, meanwhile, ours is about pathway search, so we get feedback from them after they used our software. Our results also inspire them at the same time.


One of their suggestions which had a great influence on us is that we should avoid some unreasonable results putting a group on a compound and then taking it apart, which is pretty useless. So we added codes to avoid this kind of situation taking place. And we had searched the pathway from tryptophan to indole they used, but we didn't get a practical result, for example, there will be some pathways fall into the cycle. Thus, we realized that the database we used had limitation.


DFS

Fig14.1 Collaboration between Tongji_China



For Tongji_China, they tried to improve the synthesis of indigo. The method of finding new pathways could be found through reading literature, experimental attempts through the combination of existing pathways, or simulated synthesis through software design and retrieval. Therefore, we provided help in software retrieval. Since the data in the synthetic indigo pathways are already published literature or the experimental materials needed are too expensive and not suitable for synthesis, we did not find useful results in the existed database. However, the upstream and downstream information about indigo we found provided certain reference and support for their experiments. They also tried to give us their attempts to enrich our database for designing more efficient and useful pathways.


Later, they completed their synthesis pathway design based on serval published pathway, and we also have optimized our software. Here they tested our software by searching their pathway, the search result provides us a sample of comparison between software and traditional experiment.



DFS

Fig14.2. The indole synthesised by Tongji_China





COLLABORATION 2:UESTC_Software

The software team of UESTC does the integration of various parts databases, taking iGEM parts database of the main body of the integration, which is very convenience for users to search related information. Not only can integrated information of database improve the efficiency of searching, but can also provide other software teams with a strong data support, and our collaboration is based on data. What we do is to complete the pathway design part, from the reaction to the catalytic enzyme, and then to the choice of regulatory parts. For the regulatory parts, different users can have different options according to the experimental requirements. We want to establish the regulatory parts database and build a search engine, so that the user can retrieve the corresponding parts according to their own needs. UESTC software team has done the data collation of iGEM parts database, so we established cooperation with them. They provided us with data support, which reduced our workload. What’s more, we provide the link to their software where users can get more complete information of selected parts.



DFS

Fig15. Software logo of UESTC_Software





COLLABORATION 3:CAU iGEM

The cooperation with China Agricultural University is based on their demand for detail information of their pathway, and it is also an attempt to apply our software into practice. What they did was to synthesize Astaxanthin from glucose which comes from the degradation of cellulose, and the synthetic pathway was retrieved from the literature, but the information available from the literature was limited for the technical team, and searching through the database was a time-consuming process. So, we tried to search the software for possible pathways from lycopene to Astaxanthin. Finally we provided them with a PDF of the results of the software search, from which they got some reliable information for their experiments. With our help, they felt amazed to have access to information that was not expected from the literature, and it would be interesting to see if the results of the software search performed better than those of the literature, but this verification is subject to time, so if possible, we can do this verification completely after iGEM.



DFS

Fig16. Collaboration between CAU_China





COLLABORATION 4:SJTU-software

SJTU-software contacted us to make collaboration about the use and function of software, so we organized a seminar face to face in Shanghai Jiao Tong University. In the conference, we also invited UESTC_Software to join us online. Each team showed what they do, which data they use, what function they have and how to use their software just like a demonstration. After the presentation, we talked about the problems existing in the software, and put forward some advice for each team. For UESTC_Software, their software is complete and friendly to users. We give them some suggestion in details. For SJTU-software, we give them some technical instruct. We use the same frame to build our software, so we show our source data, and explain it to them. For us, we realized the disadvantages of login function from their advice, which we based on to add the comment to each result of user get.



DFS

Fig17. Collaboration between SJTU_software





COLLABORATION 5:PROMOTION of SYNTHESIS BIOLOGY

SASTRA iGEM invited us to participate in their manufacturing of their magazine, and our collaboration forms included but was not limited to writing articles about synthesis biology and experiment, providing interviews with professionals, making the theme of synthesis biology and taking related photography.

Washington iGEM invited us to participate in the manufacturing of their audiobook which is about biology. We mainly do some translation and recording work for them, thus making chinese students what synthetic biology is and join some interesting experiments.