Technical standard

Introduction

We establish two RFC (Request for Comments) documents this year. They are the basis of the Circuit+ database. We tried our best to make the definition of a gene circuit, especially for those that contain some logical regulatory modules like gene AND gate. As a result, a circuit is well defined and the relations of individual part in circuit can be definitely clear.

RFC 101

The first technique standard, RFC 101: Logic Gene Module Standard, gives the definition of a logic gene module. This is a very important part of genetic circuit in Synthetic Biology fields. And the logical relations in genes and electric circuit can be seen as the original idea of synthetic biology. We’ve noticed that many gene circuits that were mentioned in previous iGEM projects lacked of a logic module description. They didn’t pay attention to the concept of a logical device and simply constructed their circuits. We built up the standard for promoting the concept of logic functional modules in gene circuits that are corresponding to the concept in electronics.

RFC 102

The second technique, RFC 102: Logic Gene Circuit Standard (version 2.0), gives a more detailed and normative definition of a genetic circuit. A logic gene circuit has a higher level than a gene device. In order to make this definition, we firstly define coding-frame. A coding-frame is a DNA sequence which has at least one RBS, at least one promoter, at least one protein domain, at least one terminator. A genetic circuit contains one or more than one coding-frames and can consist one or more than one plasmids. It can be regulated in many different pathways. It can accept various input signals followed by giving various output signals. Most importantly. In this RFC, we also give a standard format to record a circuit. Please see RFC 101 for more information. This standard is an update of RFC 97: Logic Gene Circuit (version 1.0), which was published by us at the end of September.

Database

Introduction

To record the standard circuits, we set up a database. The information and format follow strictly the RFC 102. And this database is open and dynamic. You can upload your circuits into the database and download information from it. We also provide APIs that allow developers to use the information of the database for other software.

Structure

So far, we’ve collected a number of valuable information from iGEM wikis and the journals about their respective gene circuits. And we set up a central database which can store all these useful information. Referring to the RFC document, all the information of a circuit can be separated into following parts:

Classification

Each circuit should declare their first classification and the secondary classification based on functions. A circuit should also be attached with some key words which can search and classify easily. Furthermore, the circuit should also be attached with the tags in Mind Map so that the circuit can be found in it.

Basic information

In part I, we store the name, the authors (or the team name), the id, the tags, the classification, the reference (wiki link or ISSN) as well as the description and applications about the gene circuit. Also, it contains the chassis (where the circuit functions), plasmids (the vector, may have more than one plasmid), the input and output of the gene circuit and the result of the circuits. Through this part, you can generally have a concept of what’s the functions of the circuits.

Circuit Structure

Based on the Technique standard, we build up a plug-in named Logical Genetic Diagram. The LGD can dynamically illustrate the structure of a gene circuit. So we need several data to build up the structure. The database record the information of the coding-frame which is the subpart of gene circuit. The information is composed of the output, input as well as the state (E.g Is this coding-frame constitutively express or it will just activated by some specific substance) and the sequence. The database also stores the biobrick assembly to coding-frame, which gives the assembling order of the biobricks and some detailed information of these biobricks. What’s more, all the regulation information (such as the gene expression, the external stimulation and the combination and degration of the substance) has been recorded in the database so that LGD (Logic Genetic Diagram) can show them.