Team:SJTU-software/Integrated
Idea
During the discussion phase of the project topic, we checked each database in iGEM and discussed with the professor to understand the latest scientific research needs for the database. In our query, we learned that the plant related biobrick database in iGEM has not been updated for three years (most recently in 2016). And a multi-functional integrated plant database is necessary for botanists. Considering the value and significance of the database, we first came up with the idea of establishing a photosynthesis database. Its main function is providing relevant information about genes and enzymes related to photosynthesis. predict enzymes based on substrates.
Preliminary Investigation
We consulted with the Chinese iGEM team that uses plant chassis and intends to produce natural plant products in a synthetic way and got their advice.
The FAFU team used Arabidopsis as the experimental chassis. They explained the specific workflow of the plant-based iGEM team. They also asked us some specific needs. For example, they hope to get more clarity. The plant is the part information of the iGEM of the chassis. They told us that the iGEM official plant collection page is no longer updated, and the chassis information in the classification is difficult to retrieve. This allows us to further refine the iGEM's plant-related part list information.
The Tongji iGEM team showed us the synthetic biological processes for the synthesis of plant products. They said that the reaction metabolic pathway is of great concern to them. The critical pathway will have a great impact on the production of the corresponding products, and the modification of the pathway based on the original pathway has certain reference value.
They mentioned that it would be difficult to find the information manually. The database provided by iGEM website can be used to find the biobricks, but it is not comprehensive, inconvenient and has stopped updating, so it is not a good choice. On the other hand, in the process of project design, not only biobrick information is needed, but also information about genes, enzymes, reactions and metabolic pathways. However, after our search of plant-related databases and relevant research literature, we found that the major databases now have their own different problems. For example, PMN database sequence is not complete, there is a lack of information. So our goal is to build an integrated global database of plants. They asked us about some of our specific needs in the plant and the metabolic pathways that we were very concerned about. On this basis, we further developed a more comprehensive integration of biobrick data based on the plant database provided by the official website of iGEM and planned to add a search database for plasmids to facilitate users to query and build suitable plasmids.
After the theme of Phosyme was preliminarily determined, we asked Prof. Fei Tao of SJTU for advices. With the concept of combining biocatalysis and synthetic biology, he aims to develop green production technology of high-value compounds, and takes photosynthetic microbial system and anti-microbial system as the main research objects to study the development of metabolic engineering tools and the construction of efficient artificial biocatalysis system. We told him about Phosyme's initial ideas, and professor Tao analyzed the feasibility and practical requirements of the plant experiments, as well as a number of recommendations for improving user friendliness. He suggested that we should develop and add visual elements to improve the user's convenience for botany research. Through communication, we understood the improvement direction of the project and had a clearer design idea. In our project last year, there was an aspect of SBML visualization, and the feedback was that there was no effective conversion and no connection to common international standards. So in Phosyme this year we have made further improvements to SBML visualization tool. In addition, our smlies code visualization from last year was applied in the company visualization direction this year.
In order to promote our project and user friendliness, we got in contact with Professor Dabing Zhang, whose main research interests are the molecular regulation mechanism of rice reproductive development. As a researcher who needs to use various databases in the research process, professor Dabing Zhang's suggestions are very insightful. At his advice, we made the search box more intuitive and detailed classification, so that users can directly understand the features of our project and make their own inquiries.
Improve
In mid-August, we took part in the 6th CCiC. We had the opportunity to give a short introduction to Phosyme and listen to presentations from other teams, which allowed us to identify common elements between our project and those of other teams. Work sharing and discussion led to the opportunity for collaboration in turn. We had an in-depth conversation with several other teams and asked for their opinions on the project. The judges talked with us about some specific needs of plant synthetic biologists and suggested to us to expand the data sources so that our database can serve more plant synthetic biology researchers. They suggest that we increase the function of the database to provide more powerful help for the research on plants, which would make our project more meaningful and practical. After the CCiC, we further refer to the related literature about the study of plant and plant of synthetic biology, figured out that the photosynthetic carbon sequestration is a hot direction of current research in plant, including the enzymes and metabolic pathways of photosynthetic carbon sequestration research is Paramount. However, compared with a limited number of substrates, enzymes in the metabolic pathway tend to have multiple choices. The diversity of enzymes makes people pay more attention to the selection of enzymes. Therefore, we decided to add the function of prediction of enzymes based on substrates and score the enzymes according to the scoring mechanism, to obtain enzymes with higher conversion efficiency and more in line with the research objectives.
Advice and Feedback
Professional Advice--Professor Dabing Zhang
We contacted professor Zhang again to discuss what to expand and what tools to add. He suggested that we classify plant data into categories such as organs and add more visual interfaces, which allows users to find the information they want more intuitively. Therefore, we added the query of plant matter granules and part of iGEM plant chassis.
Professional Advice--Professor Lida Zhang
We consulted another researcher Dr. Zhang from the school of agriculture and biology. His research direction is the deep mining of omics big data, the network modeling of biological macromolecule interaction, and the functional identification of plant resilience genes and components, which are more closely related to our database. So in the communication, he gave us a lot of meaningful advice. He suggested that we link the database to the literature, such as the links that accompany the discovery and description of each gene. And add the data about the three-dimensional structure of the enzyme to the database. For the design of metabolic pathways, he hopes that we can let users design their own pathway images to enhance the user experience by enhancing interaction. In addition, he reminded us of the compatibility of the project's use on different devices. In addition to the function of prediction of enzymes based on substrates, we also added modification of SBML metabolic pathway and the smiles visualization tool.
Feedback
We consulted the iGEM teams from China who used plant chassis and who intend to product natural plant products in a synthetic way, hoping to get their advice. We sent the completed database to them for testing and received effective feedback.
The feedback given by iGEM team of Shandong university is that in Meta Database, the retrieval speed of general keywords is a little slow, but for keywords with a small scope of coverage, the search feedback speed is faster. For the smile Drawer interface, the query results are accurate, faster and better. But for users who didn't know SMILES before, visual predictions of some complex structures are harder to make.
We have also provided Phosyme to the USTC iGEM team for testing, and they have provided a number of recommendations for detailed improvements. They also think that the introduction of SMILES and SBML should be added to help users better understand and use the visualization plug-ins. Additionally, use instructions can also be given in the input option. More search categories can be provided on the web, such as adding BBAID searches to enhance usability. SMILES' 3D visualization can also be added to provide a better user experience.
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SJTU - software
