Team:SJTU-software/Description

Inspiration

One member of our team majors in plant science. When he started to get into iGEM, he was very concerned about the plant sector, especially plant synthetic biology. Furthermore, iGEM has begun to pay more attention to plant synthetic biology and has launched the Best Plant Synthetic Biology Prize by 2016, emphasizing the importance of plant synthetic biology.

However, after reviewing a lot of information, we found that while plant synthetic biology has developed rapidly in recent years, the tools and the information web pages for the plant synthetic biology are not comprehensive enough, still often failing to predict many of the complex and lengthy synthesis pathways for specialized metabolism in plants [1]. We also found iGEM's plant-based chassis part information is no longer updated after 2016. More over, some other plant synthetic biology information in the iGEM official website has not been updated in time. That had been mentioned for several times, when we talked with teams working or having worked on plant chassis.

Q : How to deal with these problems?

A : For this question, our answer is our project Phosyme!

Our Project : Phosyme

What is Phosyme?

PHOSYME is an integrated plant Biobricks and Plant metabolite database, with some corresponding tools specifically for plant synthetic biology.

What can Phosyme do?

Phosyme can provide data support for plant metabolism research. It contains more than 100 species and more than 20,000,000 records about compound, gene, enzyme, reaction and pathway, integrated from PMN[2], NCBI, TAIR[3] and KEGG database. By walking around this world map of plant metabolism, you can choose multiple sources such as reaction pathway to get the relevant content of enzyme gene. Phosyme also contains information on the overall metabolic network, including the system biology markup format files for these species. These documents provide a model for the metabolic networks of these organisms, which can help researchers better analyze the relationship between the whole organism and their desired metabolic pathways. For researchers who want to be able to use information about plant metabolic pathways and key genes, like intending to product synthetic plant natural products, Phosyme can provide some helpful information. To better help pathway design, Phosyme also provides tools for metabolic network modification[4]. Users can modify files in SMBL format online, simplify, and export that in multiple formats. Users can also convert SMBL format files to met format files (a format we have developed for easy abbreviations and modifications in metabolic network ) , or convert met files to SMBL formatted files.

Phosyme can also provide data support for iGEM project using plant chassis. It contains around 1000 parts and 1720 backbones used on plant chassis, integrated from iGEM and addgene database.

These information can not only be retrieved , but also be browsed. The part information is listed on our specific webpage, and the researchers can inspire their new design inspiration by browsing through the components that the iGEM team once completed in the plant chassis. Besides, Phosyme still has some other tools like visualizing compound molecules online or predicting the probability bewteen enzyme sequence and compounds.

In order to promote synthetic biology and iGEM to the public, we also developed a synthetic biology room escape game. Players can learn about synthetic biology in the game. In this interesting science manual, users can learn some basic knowledge about synthetic biology. And in the secret room escape game, the key to escaping is to use these basic knowledge to solve the corresponding puzzles. The students first learned the knowledge, and then further consolidate what they learned in the game, with entertainment.

Why Phosyme?

KEGG? Only the data that has been verified in the Kegg database lacks some predictive data content. At the same time, kegg's plant page index is not clear enough, and there are some inconveniences in finding the unique metabolic pathways of each plant.

PMN? PMN database sequence is not complete, there is a lack of information.

iGEM? iGEM's plant-based part list and other advisory information on plant synthetic biology have not been updated since 2016. At the same time, due to the incompleteness of the chassis data and the category data in the part data in the iGEM database, some iGEM part registry-based searches cannot accurately retrieve the part data that was once applied to the plant chassis.

Phosyme updated the iGEM part on plant chassis list and integreted information from KEGG, PMN, TAIR and NCBI!

Go on Phosyme!

Please click to go on our website and try for it!

Reference

[1] James G. Jeffryes, Samuel M.D. Seaver, José P. Faria, Christopher S. Henry, A pathway for every product? Tools to discover and design plant metabolism, Plant Science, Volume 273, 2018, Pages 61-70, ISSN 0168-9452, https://doi.org/10.1016/j.plantsci.2018.03.025.
[2]Schläpfer, P., Zhang, P., Wang, C., Kim, T., Banf, M., Chae, L., Dreher, K., Chavali, A. K., Nilo-Poyanco, R., Bernard, T., Kahn, D., Rhee, S.Y. (2017) Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants. Plant Physiology. 173(4):2041-2059.
[3]Tanya Z. Berardini, Leonore Reiser, Donghui Li, Yarik Mezheritsky, Robert Muller, Emily Strait and Eva Huala The Arabidopsis Information Resource: Making and mining the "gold standard" annotated reference plant genome. genesis 2015 doi: 10.1002/dvg.22877
[4]GEMtractor: Extracting Views into Genome-scale Metabolic Models Martin Scharm, Olaf Wolkenhauer, Mahdi Jalili, Ali Salehzadeh-Yazdi bioRxiv 790725; doi: https://doi.org/10.1101/790725

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SJTU - software