iGEM, short for International Genetically Engineered Machine, is a worldwide synthetic biology competition. For iGEM, its philosophy for synthetic biology is based on standard parts. Simply speaking, the standardized parts contains the standard enzyme cutting sites. In this way, these standard parts could connect together just like bricks. Notably, iGEM is developed out of student project conducted during MIT’s Independent Activities Periods in 2003 and 2004. From this, we can see the influence and energy of MIT!
Considering my major, I joint iGEM software division, doing something about bioinformatics and synthetic biology based on standard parts. In last year, our team, UESTC, built three projects, Nebula, Transpeeder and iBrick.
Nebula(Network of Elaborated BioBricks based on User Locating and Automation) is a biological circuit design tool composed of Auto Mode & Manual Mode. The original idea is from me. That I want to visualize all the available circuit composed by BioBricks, looking like a nebula map. However, I found the solution based on HTML5 WebGL is too difficult. And other platform API, like Google earth is also limited. So in the end, we couldn’t reach our original goal. However, visualization is one thing, we did more important job. It’s doing new classification according to parts features for the parts database. That’s meaningful for experiments!
Transpeeder is bioinformatics tool, which help users increase or decrease the gene translation speed. The based theory is from one nature paper. The paper demonstrates that the anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Just according to this basic, one-line principle we change gene sequence without changing its production to increase or decrease its anti-Shine-Dalgarno sequence ratio and effect gene translation speed. To be honest, the theory is simple. We only considered one factor. But, in our validation experiment, the results showed that Transpeeder indeed works! Maybe we really found one of the key factor? That must be big fortune for research!
iBrick a video game on iOS platform, Bacteria VS Phages, is simple but propagates iGEM ideas.
Personally speaking, I joint iGEM community totally be chance! Maybe the inside reason for me is that I prefer to do some competition academically and even it’s interdiscriplinary. Because I think doing something interdiscriplinary is a good way to learn new things, some are knowledge itself, some are learning skills. I believe knowledge is intrinsically interdiscriplinary.
After last year iGEM jamboree, I did a lecture about my personal iGEM journey and the slideshow can be found here
This year, I performs a advisor. But I also code a little for the project. The giant iGEM jamboree in Boston is around the corner. Really looking forward it…