Motivation

Synthetic biology is now meeting its golden age. Under the spirit of give, get and share, many standards have been set up and several websites have been put online. It is the ideas of standardized and modulated, which was borrowed from electronic engineering, that allow synthetic biology to prosper. For example, Registry of Standard Biological Parts (http://parts.igem.org/) based on standard parts, together with iGEM, promotes synthetic biology a lot among undergraduate students. However, we find that not every part has high quality, for the standard cannot support some level of DNA in synthetic biology and therefore many complicated parts are marked as “composite part” and there was no standard and database for genetic circuit. We can see from IT industry that, new, proper standards can always strengthen the industry and in every step of development of IT, there is a classical standard with it. To make the language of synthetic biology more precise, to coordinate with the original idea of synthetic biology that we can see the behavior of genes just like the relations in circuit, we proposed two technique standards about logical gene module and genetic circuit. Inspired by the idea of Registry of Standard Biological Parts, we also give a solution to record and share standard genetic circuits online, that is Circuit+.

Actions

So, here are our actions

Technique standard and Database

We proposed two technique standards this year (RFC 101 and RFC 97) to give accurate definitions of logical gene module and genetic circuits. The standard of genetic circuits is very powerful and works as the theoretical base of the software. The standard of logical gene module deals problem of regulation relations and you can see it in LGD (Logical Genetic Diagram). We designed a database carefully to record the circuits we find in a stand format And many software share the same central database.

Circuit+

We develop Circuit+ as our weapon to promote the idea and standard. So, it works like Registry of Standard Biological Parts. It is website of circuits’ information and behind it is the well-built database. And you can find many ways to browse and find a certain circuit. For open and sharing, SBOL is used in the data-exchanging interface of the software and users can upload and comment circuits. To provide information of regulatory relation, LGD (Logical Genetic Diagram) is always ready when you read detail information of circuits.

Clotho application: Circuit List and TTEC

We transplant the software into Clotho and the name of the application is Circuit List. Since Clotho is a popular framework in synthetic biology, many people can experience our standard and software. The database is the same as the online one and the information is the same as the online one. We also transplanted TTEC, which is the last year iGEM software into Clotho, which is promoted by iGEM.

Synthetic biology laboratory management

Human practice

We mainly did some human practice about publicity of synthetic biology so that more people can know what synthetic biology is, what iGEM is and what our standard and software is. Some workshop meetings were made to support other teams and get help from other teams.