Team:SJTU-software/Demonstrate
Welcome to Phosyme developed by SJTU-software.
Phosyme is an integrated plant Biobricks and metabolic pathways database, with some corresponding tools specifically for plant synthetic biology.
In the following, plant synthetic biologist Prof. G will demonstrate how to use Phosyme.
Phosyme have three main functions – Database, Toolbox and Information.
Database
I. Partdata
In past few years, many iGEM teams used plant chassis in their project and made contribution to the development of plant synthetic biology. They have experimentally validated many parts in plant chassis. In our Partdata, you can search for your interested iGEM parts used in plant chassis.
For example, prof. G wanted to express GFP(Green fluorescent protein) in the plant, so he chose the description and typed in the key word “GFP”.
II. Plasmid Data
However, the biobrickes searched in Partdata are limited to iGEM project. There are also many synthetic biology plasmids for use in plants contributed by research labs around the world. In our Plasmid Data, you can search for these plasmids.
Prof. G then switched to Plasmid Data and typed in again. Finally, he found the specific plasmid which he needed.
III. Metadata
Prof. G wanted to know the information of jasmonate and its derivant in Arabidopsis. He input "jasmonate" and got the reaction relevant to it. He found that in "RXN-745", jasmonate is the product, but in "RXN-10450", it is the reactant. He wanted to know more about the pathway relevant to these reactions. He also obtained the pathways related with the compound (thiamine salvage IV and hydroxyjasmonate sulfate biosynthesis) and got a more comprehensive view of jasmonate metabolism in Arabidopsis.
In addition, prof. G also wanted to know how to synthesize heliocides. He put "heliocide" into the search bar and found the related pathway. By clicking the link in these information, he got a more comprehensive view of jasmonate metabolism in Arabidopsis.
Toolbox
Phosyme is not just database. There are also many corresponding tools waiting for us to explore.
I. Prediction
Whether enzymes in plants can react with substrates is a research hotspot, especially in the field of synthetic carbon fixation pathway. The Prediction tool uses enzyme sequence and the SMILES of the substrate to predict the reaction probability, so as to help biologists find the corresponding enzyme and substrate related to carbon fixation better.
Prof. G read a literature “A novel direct homogeneous assay for ATP citrate lyase”, which mentioned the following reaction:
ATP + citrate + CoA <=> acetyl-coa + ADP + oxaloacetate + phosphate
Actually, the reaction is outside of our model training dataset. He chose the reaction to test the performance of PREDICTION function. He typed in citrate lyase amino acid sequence and CoA SMILES code. He found that the probability value predicted by our model was 0.997, which was consistent with the reality. Then he just randomly selected enzyme sequence and substrate. In the second case, the predicted probability value was very low.
II. Visualization
The tool can provide you fantastic 2D and 3D visualization of compounds structure.
Prof. G harvested the compound using the database in our website. He also wanted to know the structure of the compound, so he used the visualization tool to understand the structure of it.
III. Netmo
Our Netmo can modify plant metabolic network models to help you better design the pathways.
Prof. G uploaded a model which he wanted to modify. Then he discarded a subset of the model’s reaction. Finally, he chose the enzyme-centric network and exported the simplified model as csv format. He obtained a concentrated model, which may improve subsequent computations dramatically.
Information
During the database search, prof. G can consult our Information to gain an integrated understanding of plant synthetic biology. This helped him better design his own experimental research.
After all the research, prof. G finally had a chance to relax. Let’s enjoy the 3D game " Dr. Chen’s Secret " and learn more about plant synthetic biology with joy!
Presented by
SJTU - software
