Team:USTC-Software/Contribution

Contribution

At the very beginning of our team's plan, we went to our school's wet lab, Team USTC, to learn something about synthetic biology. During our stay, we recognized that biobricks is very important, considering we must design software which could greatly help with experimenters working with biobricks. We asked our wet lab concerning what's the most difficult and was replied that they often found it troublesome when deciding to use which kind of biobricks, so we thought we should work out this problem. With this belief, we complete our software, contributed much to the iGEM community. Several contributions can be listed as follows.

Biobricks Recommendation

Due to the troublesome issue just mentioned, we planned to designed a biobricks recommendation system, and surely we made it. The system is based on the user's editing, namely, adding deleting and changing while using our integrated biobricks' database. According to the history, and applying our special designed algorithm, our system can give precisely prediction of biobricks that users demand.

Users can find their best biobricks instantly by our well-designed algorithm. Thus, with another metabolites prediction function insert, our software is able to greatly lessen the users' searching pressure. By using our software, user can both acquire their biobricks in a very short time without any needless thinking and get the best metabolic net design immediately. We are sure synthetic biologists can greatly benefit from us biobricks recommendation system.

iSTC-A Board Game Introducing Biobricks

To promote public awareness of synthetic biology and introduce its basic ideas to the laymen, our team is devoted to the development of a board game which aims at instructing non-biologists to understand what biobricks can do and how can we use them to make new things. Compared with other syn-bio relating games, ours is more significant because we deeply integrate the gameplay and iGEM concept together. For example, we made biobricks the core element in our board game, and our game is elaborately designed to satisfied both specialists and laymen.

Validated Contribution

The following statements describe what our work can perform. if you want to know more, please go to the Page Result.

After several months of hard work by all team members, we built the model and completed the whole project. And then, we successfully verified several ideas mentioned in some papers, which proves that our tool can works correctly as we thought. It turns that our project is useful.

Biology students and some of the professors mentioned that it's hard for them to know what will happen precisely in a cell if they edit genes. They don't know whether adding or knocking out a gene will influence other reactions in the cell. Of course, they can cultivate certain strains to examine the production rate, But the whole process would be complicated and time-wasted. Our project can precisely predict which gene is unnecessary by in silico flux analysis, thus saving time and effort.

In addition to the excellent architecture to provide an easy-to-use process, our software also considers a lot of biological logic in the output, making the output closer to real needs.

Our project has many attractive features that distinguish it from others, and we have used many experiments data to validate each of them:

1. Accurate recommendation:
If synthetic biologists want to increase the production of particular metabolites, they need to consider what types of genes should be knocked out and what kinds of genes should be overexpressed, considering the growth and survival of the microorganism. Due to the different conditions and uncertain factors, it's nearly impossible to predict the precise production of specific metabolites. However, we can precisely predict what genes will possibly influence the objective metabolite through in silico simulation.

Moreover, our software can recommend genes the biologists to overexpress or knock out to achieve their goals. Through calculation, our tool will precisely minimize the range of genes that may have a positive effect on your goals. After calculation, we can present several clear tables to show the results.


2. Precise prediction:
Before the synthetic biologists begin their experiments, our software can simulate the process and precisely predict how the flux of all metabolites, especially coenzymes, will change. For example, if they know the flux of ATP will probably reduce significantly, they might improve the culture condition or change some promoters to achieve their goals.

Biomass declined

Know more Click Here.

References

  • Figure 1: http://www.netimperative.com/2019/04/facebook-sheds-light-on-news-feed-and-advertising-algorithm-secrets/