Team:SUSTC-Shenzhen-B/technique.html

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<div class="span3 bs-docs-sidebar">
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   <li class="active"><a href="#overview">Overview</a></li>
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                                                <li class="nav-header">Technique Standard</li>
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   <li><a href="#background">Background</a></li>
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   <li class="active"><a href="#about">About This RFC</a></li>
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   <li><a href="#introduction">Introduction</a></li>
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                                                <li><a href="#purpose">Purpose</a></li>
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                                                <li><a href="#relation">Relation to other BBF RFCs</a></li>
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                                                <li><a href="#copyright">Copyright Notice</a></li>
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                                                <li><a href="#contents">Contents of Genetic Circuit Standard</a></li>
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                                                <li><a href="#author">Author’s Contact Information</a></li>
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</div>
<div class="span9">
<div class="span9">
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                                         <div id="overview">
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                                        <h1>Technique Standard</h1>
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<h2>Overview</h2>
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                                         <div id="about">
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<p>Our project, 3 Miao BioCommunity, is different from all the iGem software projects in the past, for we have an ambition to create a community for the whole synthetic biology. This community is based on our original idea, the Mind Road. Mind Road is a net structural mind map that can help users think and share ideas, which can function as a platform for all synthetic biology ideas exchange. </p>
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<h3>About This RFC</h3>
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<p>Based on the Mind Road, our community now has a theme—— share ideas. With this theme, we intend to build our 3Miao BioCommunity. In this community, we offer LGD and TTEC as useful tool for users to process the ideas. LGD is a genetic circuit designer which can present the logical relationship of related parts. What is more, users can also post their own ideas and comment on others’ work, like Facebook and Twitter.</p>
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<p>We have submitted the Request For Comment: Genetic Circuit Standard.</p>
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                                        <h5>Author</h5>
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                                        <p>Jiankui He, Yin Tong, Xiaodan Zhu, Hanrun Li, Huiyu He,  
 +
Lingjue Wang, Zhuangdian Ni, Liqun Zhou, Sisi Wu, Yi Wan, Lihua Zhang</p>
 +
                                        <h5>Submission date</h5>
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                                        <p>September 26, 2013</p>
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                                        <h5>Title</h5>
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                                        <p>BBF RFC97: Genetic Circuit Standard 1.0</p>
                                         </div>
                                         </div>
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                                         <div id="background">
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                                         <div id="introduction">
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<h2>Background</h2>
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<h3>1.Introduction</h3>
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<p>Before we got our idea, we had reviewed all the software projects of the last three years and classified them into 6 categories (fig1). As showing in the picture, designing CAD takes up the majority of these projects. As expected, most of them share the similar ideas. After a certain time of thinking, we found that it is really reasonable that iGem software projects can hardly be quite innovative, for the lack of professional knowledge and the limitation of the usage of software during synthetic biology study. But also, if we continue to follow these ideas, our project is far away from being creative or original. Then it occurred to us, why don’t we write a program to help at least the wet lab members to get new ideas? Thus, we decided to make a difference, to create our own Mind Road—— a net structural mind map—— to assist either iGEMers or professional synthetic biology researchers to come up with and share their ideas.</p>
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<p>Current, there is well adopted documentation of biobricks. The Registry of Standard Biology Part set the standard documentation for biobrick. However, there is no standard way to document a genetic circuit, what information should be included in a description of a genetic circuit. We have therefore develop the technique standard for recording a genetic circuits. This standard should help the sharing of genetic circuits information among synthetic biology community.</p>
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<p>Even though the mind map idea is good, it is not good enough. What’s more, comparing with computer software, synthetic biology lacks such community for knowledge and skills exchange, like GitHub. So setting Mind Road as the theme, we decided to take a bold step, to establish a simple and free online platform with high interaction ability intended for everyone interested in synthetic biology.</p>
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</div>
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                                        <div id="purpose">
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<h3>2.Purpose</h3>
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<p>In order to make a distinct network which aims to help everyone to obtain the necessary information of a Synthetic Biology project, we set up a new genetic design standard---- Genetic Circuit Standard.</p>
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</div>
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                                        <div id="relation">
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<h3>3.Relation to other BBF RFCs</h3>
 +
<p>Some parts of this paper reference the content of BBC RFC 89.</p>
 +
<p>Here we give a brief comment to RFC 89: This technical standard is a tidy edition of the Biobrick&trade; 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.</p>
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</div>
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                                        <div id="copyright">
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<h3>4.Copyright Notice</h3>
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<p>Copyright&copy; the Biobricks Foundation (2013). All Rights Reserved.</p>
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</div>
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                                        <div id="contents">
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<h3>5.Contents of Genetic Circuit Standard</h3>
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<h6><a href="#def">5.1 Definition of Genetic Circuit</a></h6>
 +
<h6><a href="#fun">5.2 Fundamental Component of Genetic Circuit</a></h6>
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<h6><a href="#des">5.3 Description of the Genetic Circuit</a></h6>
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<h6><a href="#cat">5.4 The Categorization of Genetic Circuit</a></h6>
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<h6><a href="#eva">5.5 The Evaluation of the Genetic Circuit</a></h6>
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<h6><a href="#exp">5.6 The Experimental Data</a></h6>
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<h6><a href="#sou">5.7 The Source & Reference</a></h6>
 +
<h6><a href="#miao">5.8 The Minimum Information of Submitting a Synthetic Biology Project on Biomiao Community</a></h6>
 +
<h5 id="def">5.1 Definition of Genetic Circuit</h5>
 +
                                        <p>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:</p>
 +
                                        <ol>
 +
                                        <li>A Genetic Circuit is composed of genetic Coding-frames.</li>
 +
                                        <li>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.</li>
 +
                                        <li>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.</li>
 +
                                        <li>Each Genetic Circuit should be given some labels that we can sort it into the Mind Road of the Bio-miao platform.</li>
 +
                                        </ol>
 +
                                        <h5 id="fun">5.2 Fundamental Component of Genetic Circuit</h5>
 +
                                        <p>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.</p>
 +
                                        <h5>5.3 Description of the Genetic Circuit</h5>
 +
                                        <p>The Description of a Genetic Circuit should contain following information:</p>
 +
                                        <ol>
 +
                                        <li>The function or purpose of the Circuit and how does it work.</li>
 +
                                        <li>All the components of your Circuit. [Coding-frames and the biobricks information]</li>
 +
                                        <li>The Circuit Diagram.</li>
 +
                                        </ol>
 +
                                        <h5 id="cat">5.4 The Categorization of Genetic Circuit</h5>
 +
                                        <p>We plan to sort all the circuit according to the practical function it can do. Then the Mind Road will dynamically generate a series of bubbles that contains all the submitted circuits. What submitter need to do is to write some labels that can precisely describe the potential function(s) of your circuit. (Submitter can reference our web app Mind Road).</p>
 +
                                        <h5 id="eva">5.5 The Evaluation of the Genetic Circuit</h5>
 +
                                        <p>All the Genetic Circuits should be given a probable evaluation. At present, we have three ranks.</p>
 +
                                        <ul>
 +
                                        <li>The 1st rank: The circuit is reported to be functional in peer-reviewed journals.</li>
 +
                                        <li>The 2nd rank: The circuit is reported by one iGEM team and independently successfully reproduced by another iGEM team.</li>
 +
                                        <li>The 3rd rank: The circuit is reported by one iGEM team.</li>
 +
                                        </ul>
 +
                                        <p>In the future, we will complete the evaluation standard.</p>
 +
                                        <h5 id="exp">5.6 The Experimental Data</h5>
 +
                                        <p>The Experimental data can well prove the conditions of the Genetic Circuit—whether it successfully functions or it is still resting on a simply design or idea. The data is permitted to be updated. We don’t need specially detailed data. The protocol of lab work is enough. This part is relatively free. Share the circuit design is the most important job.</p>
 +
                                        <p>However, several things should be shown in this part of the Genetic Circuit: The cell type (chassis) which the circuit applies in (E.g: Yeast/E.coli/ES cell), the plasmids information and the construction.</p>
 +
                                        <h5 id="sou">5.7 The Source & Reference</h5>
 +
                                        <p>This part will indicate the designer of the Genetic Circuit as well as their contact Email. The reference will show the paper(s) or wiki link that provide more detailed information.</p>
 +
                                        <h5 id="miao">5.8 The Minimum Information of Submitting a Synthetic Biology Project on Biomiao Community</h5>
 +
                                        <p> All the projects MUST be uploaded on <a href="http://sustc-genome.org.cn/igem2013/submit.html">http://sustc-genome.org.cn/igem2013/submit.html</a>. To submit and share a project on Biomiao community, the contributor MUST submit following information at least: The project name; the authors; Year; Description; References (List the article or wiki site). If the project has a diagram, the contributor SHOULD send it to Biomiao work team: <a href="mailto:igem2013@sustc.edu.cn">igem2013@sustc.edu.cn</a></p>
 +
</div>
 +
                                        <div id="author">
 +
<h3>6.Author’s Contact Information</h3>
 +
<ul>
 +
                                        <li>Jiankui He: <a href="mailto:jiankuihe@gmail.com">igem2013@sustc.edu.cn</a></li>
 +
                                        <li>Yin Tong: <a href="mailto:tongyin9002@gmail.com">tongyin9002@gmail.com</a></li>
 +
                                        <li>Mike Wong: <a href="mailto:sustc.mikewong@gmail.com">sustc.mikewong@gmail.com</a></li>
 +
                                        <li>Xiaodan Zhu: <a href="mailto:zxdedgar@gmail.com">zxdedgar@gmail.com</a></li>
 +
                                        <li>Zhuangdian Ni: <a href="mailto:nileenstropy@gmail.com">nileenstropy@gmail.com</a></li>
 +
                                        <li>Liqun Zhou: <a href="mailto:jimzhou225@gmail.com">jimzhou225@gmail.com</a></li>
 +
                                        <li>Hanrun Li: <a href="mailto:lizhongminde@126.com">lizhongminde@126.com</a></li>
 +
                                        <li>Huiyu He: <a href="mailto:howerhe@live.com">howerhe@live.com</a></li>
 +
                                        </ul>
</div>
</div>
</div>
</div>

Latest revision as of 00:29, 28 September 2013

Technique Standard

About This RFC

We have submitted the Request For Comment: Genetic Circuit Standard.

Author

Jiankui He, Yin Tong, Xiaodan Zhu, Hanrun Li, Huiyu He, Lingjue Wang, Zhuangdian Ni, Liqun Zhou, Sisi Wu, Yi Wan, Lihua Zhang

Submission date

September 26, 2013

Title

BBF RFC97: Genetic Circuit Standard 1.0

1.Introduction

Current, there is well adopted documentation of biobricks. The Registry of Standard Biology Part set the standard documentation for biobrick. However, there is no standard way to document a genetic circuit, what information should be included in a description of a genetic circuit. We have therefore develop the technique standard for recording a genetic circuits. This standard should help the sharing of genetic circuits information among synthetic biology community.

2.Purpose

In order to make a distinct network which aims to help everyone to obtain the necessary information of a Synthetic Biology project, we set up a new genetic design standard---- Genetic Circuit Standard.

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.

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
5.8 The Minimum Information of Submitting a Synthetic Biology Project on Biomiao Community
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

We plan to sort all the circuit according to the practical function it can do. Then the Mind Road will dynamically generate a series of bubbles that contains all the submitted circuits. What submitter need to do is to write some labels that can precisely describe the potential function(s) of your circuit. (Submitter can reference our web app Mind Road).

5.5 The Evaluation of the Genetic Circuit

All the Genetic Circuits should be given a probable evaluation. At present, we have three ranks.

  • The 1st rank: The circuit is reported to be functional in peer-reviewed journals.
  • The 2nd rank: The circuit is reported by one iGEM team and independently successfully reproduced by another iGEM team.
  • The 3rd rank: The circuit is reported by one iGEM team.

In the future, we will complete the evaluation standard.

5.6 The Experimental Data

The Experimental data can well prove the conditions of the Genetic Circuit—whether it successfully functions or it is still resting on a simply design or idea. The data is permitted to be updated. We don’t need specially detailed data. The protocol of lab work is enough. This part is relatively free. Share the circuit design is the most important job.

However, several things should be shown in this part of the Genetic Circuit: The cell type (chassis) which the circuit applies in (E.g: Yeast/E.coli/ES cell), the plasmids information and the construction.

5.7 The Source & Reference

This part will indicate the designer of the Genetic Circuit as well as their contact Email. The reference will show the paper(s) or wiki link that provide more detailed information.

5.8 The Minimum Information of Submitting a Synthetic Biology Project on Biomiao Community

All the projects MUST be uploaded on http://sustc-genome.org.cn/igem2013/submit.html. To submit and share a project on Biomiao community, the contributor MUST submit following information at least: The project name; the authors; Year; Description; References (List the article or wiki site). If the project has a diagram, the contributor SHOULD send it to Biomiao work team: igem2013@sustc.edu.cn

6.Author’s Contact Information

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