Team:SJTU-software/Contribution

Overview

When communicating with the iGEM teams who intend to start project using plant chassis, we found that there is need for a integrated platform of plant informations. They also told us that the iGEM's part collection for plant had not been updated. Therefore, we developed Phosyme. This platform integrated the plant metabolite information from PMN, NCBI, TARI and KEGG database. It also includes the updated iGEM part list and the plasmid used in plant chassis. Meanwhile, we added some tools for prediction, viusulization and biological metabolic network modification. We still composed a game to arouses people's interest about plant synthetic biology.

Database

We developed mainly two kind of databases: plant metabolite database and biobrick database.

The plant metabolite database include compound, enzyme, gene, reaction, pathway imformation in more than 100 kinds of plants, integrated the from PMN, NCBI, TARI and KEGG database. With this database, users can find a key reaction or key gene of plant more efficiently.

And the biobrick database include the iGEM parts and the plasmids used in plant chassis form iGEM and addgene. For the page of the part using for plant in iGEM has not been updated for more than two years, we searched these type of parts and listed that in our database. The number of that is around 1,000, while the counterpart listed in iGEM is around 600.

Tools

We developed there type of tools: Prediction, Visulization and Network Modification.

The Prediction tool is developed to predict the probability between the enzyme and the substrate in photosynthetic carbon fixation with the complicated CNN model. And the visulization is used for smiles, a format of chemical compounds. With the help of our network modification tool can adjust their SBML model online, deleting some part of this biological metabolic network model and export that in 5 types of format. It is also able to convert a SMBL shorthand format to a SBML format file or conversely.

Game

In order to promote synthetic biology and iGEM to the public, we 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 escape 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 entertaining.

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SJTU - software