1.About This RFC

We submitted this RFC as BBF RFCxX: Genetic Circuit Standard 1.0. But we have not received the feedback yet.

Submission information:Jiankui He, Yin Tong, Xiaodan Zhu, Hanrun Li, Huiyu He, Lingjue Wang, Zhuangdian Ni, Liqun Zhou, Sisi Wu, Yi Wan, Lihua Zhang.September 26, 2013

2.Introduction

At present, the Parts Registry has become an extremely large database that we can find a lot of functional and practical Biobricks from it. However, the database is still a little bit scattered. So we concentrate on building a new standard which may assist people to easily find what they want. Based on the concept of Biobrick™, a new standard is built up -- Genetic Circuit Standard (version1.0). Though this new standard is still not perfect like Biobrick™, it can indeed provide a new clear approach to share your GC design and obtain some useful circuit design.

3.Relation to other BBF RFCs

Some parts of this paper reference the content of BBC RFC 89.

Here we give a brief comment to RFC 89: This technical standard is a tidy edition of the Biobrick™ standard, but if this standard are serving for the Bio-Search software, probably it need some more information about the projects that the submitted biobricks have applied in. Hope this can give some help to the team.

4.Copyright Notice

Copyright© the Biobricks Foundation (2013). All Rights Reserved.

5.Contents of Genetic Circuit Standard

5.1 Definition of Genetic Circuit

5.2 Fundamental component of Genetic Circuit

5.3 Description of the Genetic Circuit

5.4 The Categorization of Genetic Circuit

5.5 The evaluation of the Genetic Circuit

5.6 The Experimental data

5.7 The Source & Reference

5.1 Definition of Genetic Circuit

A Genetic Circuit is a biological unit which could achieve specific function(s). In Parts Registry, we found that some submitted parts can already be a functional unit. However, we consider that those parts (which contain a series of Biobricks) have disorganized the Parts Registry and we expect to DEVELOP a standard to solve the problem. The definition of Genetic Circuit can be summarized as following points:

1. A Genetic Circuit is composed of genetic Coding-frames.
2. A Coding-frame is strictly defined as a combination of various biobricks. It MUST contains four types of component: Promoter, RBS, Coding sequence, Terminator (If a component hasn’t been registered in Parts Registry, at least it should be modularized and standardized). Essentially, a Coding-frame is a DNA sequence.
3. Different Coding-frames can influence each other with expressing various molecular signals. They can also be stimulated by the surrounding factors (physical, biological, chemical, etc.). In other words, Different Coding-frames can set up a logical regular system (Such as an AND-gate relation). Therefore, a Genetic Circuit possesses outer and inner logical relations. This is what the Part Registry can’t record.
4. Each Genetic Circuit should be given some labels that we can sort it into the Mind Road of the Bio-miao platform.

5.2 Fundamental component of Genetic Circuit

A Genetic Circuit consists of Coding-frames. A Coding-frame consist of four types of biobrick in the correct order: Promoter, RBS, coding sequence, terminator. Each component should have an individual number in Parts Registry. If not, the submitter should state how you modularized and standardized it.

5.3 Description of the Genetic Circuit

The Description of a Genetic Circuit should contain following information:

1. The function or purpose of the Circuit and how does it work.
2. All the components of your Circuit. [Coding-frames and the biobricks information]
3. The Circuit Diagram.

5.4 The Categorization of Genetic Circuit

A Genetic Circuit consists of Coding-frames. A Coding-frame consist of four types of biobrick in the correct order: Promoter, RBS, coding sequence, terminator. Each component should have an individual number in Parts Registry. If not, the submitter should state how you modularized and standardized it.

5.2 Fundamental component of Genetic Circuit

A Genetic Circuit consists of Coding-frames. A Coding-frame consist of four types of biobrick in the correct order: Promoter, RBS, coding sequence, terminator. Each component should have an individual number in Parts Registry. If not, the submitter should state how you modularized and standardized it.

Introduction

At present, the Parts Registry has become an extremely large database that we can find a lot of functional and practical Biobricks from it. However, the database is still a little bit scattered. So we concentrate on building a new standard which may assist people to easily find what they want. Based on the concept of Biobrick™, a new standard is built up -- Genetic Circuit Standard (version1.0). Though this new standard is still not perfect like Biobrick™, it can indeed provide a new clear approach to share your GC design and obtain some useful circuit design.

Introduction

At present, the Parts Registry has become an extremely large database that we can find a lot of functional and practical Biobricks from it. However, the database is still a little bit scattered. So we concentrate on building a new standard which may assist people to easily find what they want. Based on the concept of Biobrick™, a new standard is built up -- Genetic Circuit Standard (version1.0). Though this new standard is still not perfect like Biobrick™, it can indeed provide a new clear approach to share your GC design and obtain some useful circuit design.