Team:Tongji Software/Attributions
TEAM
Here we are! Group photo of Tongji_Software!
TEAM MEMBERS
STUDENT
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
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
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
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
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
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
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
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
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
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
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
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
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.
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.
Jérémie Boulay Attribution
Open souce in github to support the use of Animated-mesh-lines
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.
GenScript
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.
USTC_Software
They helped us to find bugs in our codes.
CAU_China
They shared their pathway information with us, thus enabling us to verify our software.
NOTE BOOK
2018.12
Construct 2019 Tongji_Software
Team leader: Xu bo, Shi Huili
Team member: Xing Feiyang, Zhao Zexin, Liu Zhaoyang, Xu Shudi, Piao Xue, Nie Yao, Zheng Yuqiao, Liu Chengyan
2019.02-2019.03
Software track confirm
Group members get to know basic knowledge of synthesis biology
Read literature based on pathways, proteins, disease treatment, enzymes, etc., collect materials that can be used to prepare the project.
2019.03.30
Confirm the main body pathway design of our project, and the pathway search part we decided to optimize last years project.
2019.04
Brain storm for detailed functions and see whether we can solve it through literature
2019.04.13
HP:NYUSH
Have a brief idea of what other team do and share our primary idea
Improvement:
| 1 | point out where do we get the scoring matrix |
2019.05
The algorithm of pathway search part has been optimized, meanwhile we were doing some data clear job
Confirm that we have four function, and they are pathway search, enzyme selection, parts design and information share
Collaboration: Tongji_China
They tried to improve the synthesis of indigo, so they used our software to search the pathway, although we didn’t get a suitable pathway, we found that we should avoid some useless results
2019.05.10
Design team logo
the new design concept of modular design
2019.05.18
HP:CPU
We show the whole project design to judges and other team members, and we get feedback that the platform we want to build is too big, which means we can’t make every part perfect in such a short time by ourselves, so we can use existed tools in our software.
2019.05.26
Determine our software’s name: Pathlab
HP: ECUST
suggestions:
| 1 | compared with making all enzymes into one single bacterium, making the flora seems to be more practical and feasible |
| 2 | consider the influence of the external environment |
| 3 | cofactors of reactions or enzymes |
Improvement:
| 1 | put each step of the reaction of a pathway into a single engineering bacteria to form a flora |
| 2 | take temperature and pH into consideration to give a score for each enzyme |
2019.06
2019.06.04
HP: GeneWiz Company
Get some ideas about the scoring, and in the enzyme selection part, we are suggested that the selected enzyme’s physical and chemical character must be very stable, and we should take the whole process and the final result into consideration. In pathway part, we get suggestions that reactions in databases are limited, and it will be useful if our software can simulate some new reactions.
Improvement:
| 1 | novel reaction; scoring enzymes based on physical and chemical character between the enzyme and the engineering bacteria |
2019.07
Finish the primary version of our software
A game for students to have a basic idea of synthesis pathway
2019.08
Education Section: the First Poster
The first post "Programmer iGEMer is online~" is issued on the Tongji iGEM wechat public platform, which introduces the main content of our project Pathlab and the problems we want to solve.
Education Section: Presentation in Tongji University
Introduced the status of bioinformatics in life science, the functions of bioinformatics in iGEM and how to use the knowledge of bioinformatics to construct a software about synthetic biology in iGEM. This presentation made us have a new understanding of bioinformatics, and understand the application of bioinformatics in synthetic biology.
2019.08.19-2019.08.23
HP: CCIC
In the Pathway Part:
| 1 | do more work about validation, which means to prove the results we gave are believable |
In the overall design:
| 1 | know more about what users want so that we can design corresponding functions |
| 2 | the design on the web page should be more user-friendly, which means we should point out that what steps should users do. |
Improvement:
| 1 | Build a model to choose more efficient algorithm |
| 2 | Do a comparison of accuracy and run time between DFS algorithm and Greedy algorithm and we draw a conclusion that in limited reactions, Greedy algorithm performs as accurate as DFS algorithm does, but the running time Greedy algorithm used is much less than DFS algorithm |
| 3 | pay a visit to companies or institutions about manufacturing engineering |
| 4 | set a questionnaire to confirm the design of our software web page about which kind of web page do users want |
2019.08.29
Education Section: the Second Poster
The second post “6th CCiC in ShenZhen” was released in the wechat public platform Tongji iGEM, which mainly introduces the main activities of the team participating in CCiC in Shenzhen and the gains of the participants.
2019.09
The design of the webpage part mainly includes the search part, the code design of the result part, and the design and adjustment of the visualization.
HP: ECUST
| 1 | select a pathway and enzyme with special background which is used generally to show the whole workflow |
| 2 | beautify our software |
Collaboration: SASTRA iGEM
SASTRA iGEM invited us to participate in their manufacturing of their magazine, and our collaboration forms including but not limited to write articles about synthesis biology and experiment, provide interviews with professionals, and make the theme of synthesis biology or to shoot related photography.
Collaboration：UCD iGEM
We participated in UCD’s research about the use of mammals in this iGEM competition.
2019.09.05
Discuss with the project leader teacher Fei Jian on the current progress of the project.
Result: In the channel design part, users can be provided with various choices. For example, the user 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.
2019.09.06
Education Section: the Article Released on the Wechat Public Platform
The third article, "Efficient Path Finder - Alpha ant", was released in the wechat public platform Tongji iGEM. It mainly introduces the background of the project's predecessor, Alpha ant, the main algorithm, scoring standards, etc. Better understand our projects.
2019.09.10
Received a collaboration invitation from Washington iGEM, mainly about the translation and recording of audio books.
2019.09.19
Collaboration: UESTC_Software
Use their data about parts from iGEM, and we test software with each other
2019.10
2019.10.13
Collaboration: SJTU_Software and UESTC_Software
for SJTU_Software
we gave them some technical instructs, because we have used the same frame to build our software, so we show our source data, and explain it to them
for UESTC_Software
their software is complete and user-friendly, but there are some problems about the present of result
for Tongji_Software
we realized the disadvantages of login function from their advice which we based on to add the comment to each result of user get.
Collaboration：CAU iGEM
search their pathway in our software successfully