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               <a class="item">Technique standard and Database</a>
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         <h2 class="ui dividing header">Motivation</h2>
         <h2 class="ui dividing header">Motivation</h2>
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         <p>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 (<a href="http://parts.igem.org/" target="_blank">http://parts.igem.org/</a>) 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+.</p>
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         <p>Our project focuses on genetic circuits. In the last ten years, iGEM competition has produced and collected thousands of biobricks. And extensive efforts have been made to create the technique standard for biobricks. A genetic circuit usually composes of several biobricks and can perform some predefined function. Our project aim to go one step further, that we develop the technique standard for genetic circuits and build up a central database for collecting and sharing genetic circuits.</p>
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         <p>So, here’s our actions</p>
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         <p>So, here are our actions</p>
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         <h3>Technique standard and Database</h3>
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         <h3><img src="https://static.igem.org/mediawiki/2013/4/40/Standard%2832%29.png" />Technical standard</h3>
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         <p>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.</p>
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         <p>We proposed two technical standards this year (RFC 101 and RFC 97) to define logical gene module and genetic circuits.</p>
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         <h3>Circuit+</h3>
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         <h3><img src="https://static.igem.org/mediawiki/2013/a/a3/Logo%2832%29.png">Circuit+</h3>
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         <p>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.</p>
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        <h5>a central database for genetic circuits</h5>
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         <h3>Clotho application: Circuit List and TTEC</h3>
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         <p>Inspired by the Registry of Standard Biological Part database, we came up with an ambitious plan that we should make the Registry of Standard Genetic Circuit. Our goal is to collect all previous iGEM projects and all published synthetic biology projects.</p>
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         <p>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.</p>
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        <p>The ultimate goal of our project is to promote sharing in synthetic biology community! We have a future plan of establishing a community based on Mind Road and LGD, for we clearly know the importance of sharing design. To make the sharing efficient and effective, we proposed a technique standard for documentation of a genetic circuit</p>
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         <h3><img src="https://static.igem.org/mediawiki/2013/6/60/Lab%2832%29.png" />LGD</h3>
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         <p>LGD is short for Logical Genetic Digram. It is a computer aided graphical generator integrated into our database. User can see the circuits and the relations between parts.</p>
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         <p>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. We also made a survey concerned with ethic issues in synthetic biology.</p>
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         <h3><img src="https://static.igem.org/mediawiki/2013/7/71/Humanpractise%2832%29.png" />SBOL</h3>
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        <p>Our software support SBOL. SBOL is used in the data-exchanging interface of the software and users can upload and comment circuits.</p>
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         <h3><img src="https://static.igem.org/mediawiki/2013/2/2d/Clotho%2832%29.png" />Clotho application: Circuit List and TTEC</h3>
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         <p>We developed a Clotho version of circuitplus, with the name “Circuit List”. We also developed TTEC in clotho, which is originally created by SUSTC-Shenzhen-B in 2012.</p>
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Latest revision as of 03:26, 29 October 2013

SUSTC-ShenZhen-B

SUSTC-ShenZhen-B
Visit Circuit+
iGEM
iGEM homepage wiki homepage My Account Edit
Overview Standard and database
Software
Circuit+ Tutorial Safety Feedback Future Lab Manager Clotho
Human practice
Workshop meeting Publicity
Achievement
Team
About us Notebook Acknowledgement

Overview

Have a glimpse of our project.

Motivation
Actions
Technical standard Circuit+ LGD SBOL Clotho application: Circuit List and TTEC
Back to Homepage

Motivation

Our project focuses on genetic circuits. In the last ten years, iGEM competition has produced and collected thousands of biobricks. And extensive efforts have been made to create the technique standard for biobricks. A genetic circuit usually composes of several biobricks and can perform some predefined function. Our project aim to go one step further, that we develop the technique standard for genetic circuits and build up a central database for collecting and sharing genetic circuits.

Actions

So, here are our actions

Technical standard

We proposed two technical standards this year (RFC 101 and RFC 97) to define logical gene module and genetic circuits.

Circuit+

a central database for genetic circuits

Inspired by the Registry of Standard Biological Part database, we came up with an ambitious plan that we should make the Registry of Standard Genetic Circuit. Our goal is to collect all previous iGEM projects and all published synthetic biology projects.

The ultimate goal of our project is to promote sharing in synthetic biology community! We have a future plan of establishing a community based on Mind Road and LGD, for we clearly know the importance of sharing design. To make the sharing efficient and effective, we proposed a technique standard for documentation of a genetic circuit

LGD

LGD is short for Logical Genetic Digram. It is a computer aided graphical generator integrated into our database. User can see the circuits and the relations between parts.

SBOL

Our software support SBOL. SBOL is used in the data-exchanging interface of the software and users can upload and comment circuits.

Clotho application: Circuit List and TTEC

We developed a Clotho version of circuitplus, with the name “Circuit List”. We also developed TTEC in clotho, which is originally created by SUSTC-Shenzhen-B in 2012.

© SUSTC-ShenZhen-B

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