iGEM 2020 — Team Tongji_Software

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# Team:Tongji Software/Notebook

* ![](https://static.igem.org/mediawiki/2020/b/b1/T--Tongji_Software--bg.png)
* [Home](https://2020.igem.org/Team%3ATongji_Software)

Our Project

[Description](https://2020.igem.org/Team%3ATongji_Software/Description)
[Design](https://2020.igem.org/Team%3ATongji_Software/Design)
[Contribution](https://2020.igem.org/Team%3ATongji_Software/Contribution)
[Engineering](https://2020.igem.org/Team%3ATongji_Software/Engineering)
[Partnership](https://2020.igem.org/Team%3ATongji_Software/Partnership)
[Implementation](https://2020.igem.org/Team%3ATongji_Software/Implementation%20)
[Proof of Concept](https://2020.igem.org/Team%3ATongji_Software/Proof_Of_Concept)

Team

[Team information](https://2020.igem.org/Team%3ATongji_Software/Team)
[Attributions](https://2020.igem.org/Team%3ATongji_Software/Attributions)
[Collaborations](https://2020.igem.org/Team%3ATongji_Software/Collaborations)
[Notebook](https://2020.igem.org/Team%3ATongji_Software/Notebook)

* [Medal](https://2020.igem.org/Team%3ATongji_Software/Medal%20)
* [Human Practices](https://2020.igem.org/Team%3ATongji_Software/Human_Practices)
* [Education](https://2020.igem.org/Team%3ATongji_Software/Education)
* [Model](https://2020.igem.org/Team%3ATongji_Software/Model)
* [Safety](https://2020.igem.org/Team%3ATongji_Software/Safety)

Notebook

Notebook

[TOP](#top)

2019.12

(1) Set up 2020 Tongji\_Software.

Team Leaders：Zhu Jun, Jiang Wenyuan, Xiao Chunfu

Team members: Zhang Jiasheng, Zhang Chengwei, Zhu Huidi, Lin Zhifan, Ling Xinnan

2020.1-2020.2

(1) Research past projects of the software track, including Michigan\_Software, Florida\_Atlantic, SJTU-Software, NCTU\_Formosa, SYSU\_software, UESTC-Software, etc.

(2) Read the Synthetic Biology Tools and Application.

2020.3

(1) Confirm the direction of our project. We should inherit the pathway search part.

(2) The second recruitment members: Gong Ran, Fu Qianzheng, He Yining, Jin Yuyuan, Liu Muyi, Mo Wanying, Tang Yun, Wang Shangyou, Xu Yexin.

(3) Read literature about metabolism, pathways, proteins, enzymes, etc. Collect materials that can be used to prepare the project.

2020.4.1-4.15

(1) Confirm the database part, collect the data from KEGG, Brenda, ChEBI, etc.

(2) Collaboration with Tongji\_China and receive some feedback.

(3) Use questionnaires to investigate the needs of the pathway-searching tool and investigate the projects of 40 teams that participated in iGEM in 2018 and 2019.

(4) Hand over the prototype of our pathway-searching tool to two teams from Xi'an Jiaotong-Liverpool University and Nanjing Agricultural University, and we get some valuable feedback.

2020.4.15-4.30

(1) We communicated online with Professor Changsheng Du and asked for some advice on our program.

(2) Ready to make a role-playing game and spread it through the internet.

(3) Research the literature about metabolism simulation.

2020.5

(1) Confirm that we have three functions: The Synthetic Bay(database), the Pathway Finder, and the Hybrid Metabolism Simulation.

(2) Data preprocessing and integration.

(3) Confirm some details of algorithms in the Pathway Finder and the Hybrid Metabolism Simulation.

(4) Register our team.

(5) Design team logo.

2020.6

On June 13th, 2020, SYSU-Software and we had a conference online, and have been in touch ever since.

2020.7

(1) Online Educational Work in Tongji Seeding Program: we have an online meeting with 40 high school students on July 19th, 2020.

(2) The three parts of our software are improving.

2020.8

(1) Register for the CCiC.

(2) Prepare for the presentation video and poster.

(3) On August 15th, we take part in the first Conference of China Software iGEMer Community(CCSiC).

(4) Take part in CCiC from August 28th to 31st as one of all sixty teams.

(5) Game is almost ready.

(6) We five China Software teams co-host the Workshop in CCiC.

2020.9

(1) On September 22nd, we, together with SJTU-software, hold a seminar online to talk about the software’s problems and put forward some advice for each team.

(2) The first article, "The Metabolism and Health" is released in the WeChat Official Accounts "Tongji iGEM", and we receive a lot of great feedback.

(3) Our software "Synthesis Navigator" is almost completed, and we are improving it according to the suggestions we received in these weeks.

(4) The software front end is also basically completed.

(5) Cooperate with a scientific research team of Tongji University. Feng Junchen, a doctoral student in the laboratory of Professor Li Ping, provides us with rich feedback after using it.

2020.10

(1) On October 4th, SYSU-Software and we have a conference online again and hope to promote further collaboration.

(2) On October 8th, we, together with Tongji\_China, have conferences offline about the method of modeling used by them and some daily events during the game.

(3) On October 13th, 2020, we hold a science promotion activity for first-year biology students together with Tongji\_China.

(4) The second and third articles, "The Metabolic Pathway and Engineering", "The Introduction to Synthesis Navigator", are released in the WeChat Official Accounts "Tongji iGEM". We want more people to pay attention to metabolic engineering.

(5) We publish our game for some high school students and encourage them to know the concept and basic research methods of synthetic biology.

(6) Prepare for the Giant Jamboree!

CONTACT US:  tj\_software2020@163.com
ADDRESS:  No.1239 Siping Road, Tongji University, Shanghai, China
© Copyright 2019–2020 All Rights Reserved. This website was built by Tongji Software.

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# Team:Tongji Software/Engineering

* ![](https://static.igem.org/mediawiki/2020/b/b1/T--Tongji_Software--bg.png)
* [Home](https://2020.igem.org/Team%3ATongji_Software)

Our Project

[Description](https://2020.igem.org/Team%3ATongji_Software/Description)
[Design](https://2020.igem.org/Team%3ATongji_Software/Design)
[Contribution](https://2020.igem.org/Team%3ATongji_Software/Contribution)
[Engineering](https://2020.igem.org/Team%3ATongji_Software/Engineering)
[Partnership](https://2020.igem.org/Team%3ATongji_Software/Partnership)
[Implementation](https://2020.igem.org/Team%3ATongji_Software/Implementation%20)
[Proof of Concept](https://2020.igem.org/Team%3ATongji_Software/Proof_Of_Concept)

Team

[Team information](https://2020.igem.org/Team%3ATongji_Software/Team)
[Attributions](https://2020.igem.org/Team%3ATongji_Software/Attributions)
[Collaborations](https://2020.igem.org/Team%3ATongji_Software/Collaborations)
[Notebook](https://2020.igem.org/Team%3ATongji_Software/Notebook)

* [Medal](https://2020.igem.org/Team%3ATongji_Software/Medal%20)
* [Human Practices](https://2020.igem.org/Team%3ATongji_Software/Human_Practices)
* [Education](https://2020.igem.org/Team%3ATongji_Software/Education)
* [Model](https://2020.igem.org/Team%3ATongji_Software/Model)
* [Safety](https://2020.igem.org/Team%3ATongji_Software/Safety)

Engineering

[Born](#Born)

[Grow](#Grow)

[Train](#Train)

[Improvement](#Improvement)

[Reference](#Reference)

[TOP](#title)

Engineering Success

1. Born

In the early stages of the project, we used questionnaires to investigate the needs and carried out statistics on teams over the years. And we found that the problem of how to prepare compound B from compound A is a recurring one in scientific research, and scientists often spend a lot of time trying to find the right pathway from the vast amount of literature and to conduct preliminary experiments. To solve these problem, we envisioned creating a tool that would help researchers find the desired pathway from the vast amount of reaction data and allow them to perform simulations of the pathway prior to experimentation. Thus, Synthesis Navigator was born.

2. Design

In order to get the inspiration to solve these problems, we investigated many representative iGEM projects, and part of their work inspired us: Tongji-Software 2019: Their talent framework for pathway search has a high referential value for our project; USTC-Software 2018: The excellent performance of their model gives us the confidence to simulate the engineered organism's metabolic system. Then, we determined the specific function of our software. Besides, to support our complex calculation, we had to construct a database including all Reactions, Compound, and Enzyme data. More details on [Design](https://2020.igem.org/Team%3ATongji_Software/Design).

3. Grow

Synthesis Navigotor obtains pathway data from the Synthetic Bay , uses the Pathway Finder to find appropriate pathways according to the user's wishes, and finally analyzes the identified pathways through hybrid metabolic simulations. It is important to note that these three functions can be used as a whole, or any one of the tools can be used according to your needs. Our toolbox had a workflow for users' analysis. User could search the ID from database to get what you want, and then used these IDs to search for the best pathway. Finally, according to the reactions on the pathway, software would set initial states value, simulated metabolic reactions and predicted what will be changed.

4. Test and Train

To confirm the validity of the Synthesis Navigator, we searched for pathways and compared them with those in the literature.

3.1 Pathway Finder

（Note: The input weights include km, kkm, toxicity, pH, temperature, which are all 0.2.）

3.1.1 Validate with pathlab

Pathway Finder was developed based on pathlab. We use Pathway Finder and pathlab to search for pathway for the production of flavonoids from glucose, and we see that Pathway Finder finds shorter paths, which benefits from the increase in data volume and optimization of the search algorithm.

![figure1.search results in our software SynthesisNavigator.](https://static.igem.org/mediawiki/2020/0/07/T--Tongji_Software--ENG1.JPG)

figure1. search results in our software SynthesisNavigator.

![figure2.search results in 2019 Tongji_Software pathlab.](https://static.igem.org/mediawiki/2020/3/30/T--Tongji_Software--ENG2.JPG)

figure2. search results in 2019 Tongji\_Software pathlab.

3.1.2 Validate with other teams

(1) With UANL

UANL uses vanillic acid to synthesize Cis-cis-muconic via a three-step reaction, 2019. And this pathway can also be searched using PathwayFinder (the third and fourth in the figure).

![figure3.search results in UANL 2019.](https://static.igem.org/mediawiki/2020/0/0a/T--Tongji_Software--ENG3.JPG)

figure3. search results in UANL 2019（picture comes from UANL 2019）

(2) With ECUST\_China

In 2019, ECUST\_China used two enzymes, exoglucanase (cex) and endoglucanase (cen), to break down cellulose into fibrous disaccharides in preparation for the subsequent synthesis of bacterial cellulose. The same pathway was also found using PathwayFinder (the second one in the figure) and ranked highly.

![figure4.search results in ECUST_China 2019.](https://static.igem.org/mediawiki/2020/2/2d/T--Tongji_Software--ENG4.JPG)

figure4. search results in ECUST\_China 2019（picture comes from ECUST\_China 2019）

3.1.3 Validate with literature

A search of the literature revealed that one of the pathways for the synthesis of indole pyruvic acid is that L-Tryptothan is oxidized to produce the intermediate product Indole-3-pyruvic acid, which is then reacted to produce Indole-3-acetic acid. pathwayFinder also found the same pathway (Fourth in Figure )

![figure5.compare our results with article.](https://static.igem.org/mediawiki/2020/3/38/T--Tongji_Software--ENG5.JPG)

figure5. compare our results with article.

As another example, the final generation of ectoine from L-aspartate 4-semialdehyde to L-2 4-diaminobutyric acidzai to N(4)-acetyl-L-2 4-diaminobutyric acid is the practical pathway for generating ectoine. The same can be found using PathwayFinder (third in the figure)

![figure6.compare our results with article.](https://static.igem.org/mediawiki/2020/a/ad/T--Tongji_Software--ENG6.JPG)

figure6. compare our results with article.

5. Improvement

The progress of creating PathFinder was not always easy, as the misuse of ‘>’ and '<' and other minor errors in the code prevented us from searching the pathways that pathlab was able to search last year, but we eventually overcame this problem. However, there are still some problems with the tool, for example, we didn't find the desired pathways using the 2019 Evry\_Paris-Saclay data, and we think this is one of the directions to improve the tool in the future.

References:

[1] 朱夜琳. 大肠杆菌中吲哚丙酮酸的代谢工程研究[D].中国科学技术大学,2017.

[2] 龚皎. 大肠杆菌中四氢嘧啶合成通路的构建及优化[D].兰州大学,2012.

[3] ECUST\_China和UANL和Tongji\_Software三个IGEM队伍2019年的数据

CONTACT US:  tj\_software2020@163.com
ADDRESS:  No.1239 Siping Road, Tongji University, Shanghai, China
© Copyright 2019–2020 All Rights Reserved. This website was built by Tongji Software.

[![](https://static.igem.org/mediawiki/2020/8/8b/HQ_page_logo.jpg)](https://2020.igem.org)

# Team:Tongji Software/Experiments

# Experiments

Describe the research, experiments, and protocols you used in your iGEM project. These should be detailed enough for another team to repeat your experiments.

If you made Parts this year, please remember to put all information, characterization, and measurement data on the Part's Main Page on the [Registry](http://parts.igem.org/Main_Page).

### What should this page contain?

* Protocols
* Experiments

### Inspiration

* [2014 Colombia](https://2014.igem.org/Team%3AColombia/Protocols)
* [2014 Imperial](https://2014.igem.org/Team%3AImperial/Protocols)
* [2014 Caltech](https://2014.igem.org/Team%3ACaltech/Project/Experiments)

[![](https://static.igem.org/mediawiki/2020/8/8b/HQ_page_logo.jpg)](https://2020.igem.org)

# Team:Tongji Software/Results

# Results

You can describe the results of your project and your future plans here.

### What should this page contain?

* Clearly and objectively describe the results of your work.
* Future plans for the project.
* Considerations for replicating the experiments.

### Describe what your results mean

* Interpretation of the results obtained during your project. Don't just show a plot/figure/graph/other, tell us what you think the data means. This is an important part of your project that the judges will look for.
* Show data, but remember **all measurement and characterization data must also be on the Part's Main Page on the [Registry](http://parts.igem.org/Main_Page).** Otherwise these data will not be in consideration for any medals or part awards!
* Consider including an analysis summary section to discuss what your results mean. Judges like to read what you think your data means, beyond all the data you have acquired during your project.

### Project Achievements

You can also include a list of bullet points (and links) of the successes and failures you have had over your summer. It is a quick reference page for the judges to see what you achieved during your summer.

* A list of linked bullet points of the successful results during your project
* A list of linked bullet points of the unsuccessful results during your project. This is about being scientifically honest. If you worked on an area for a long time with no success, tell us so we know where you put your effort.

### Inspiration

See how other teams presented their results.

* [2014 TU Darmstadt](https://2014.igem.org/Team%3ATU_Darmstadt/Results/Pathway)
* [2014 Imperial](https://2014.igem.org/Team%3AImperial/Results)
* [2014 Paris Bettencourt](https://2014.igem.org/Team%3AParis_Bettencourt/Results)