Team:Tongji Software/Engineering
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.
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.
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).
(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.
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 )
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)
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