Team:SUSTC-Shenzhen-B/project.html

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  <li class="active"><a href="#overview">Overview</a></li>
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  <li><a href="#introduction">Introduction</a></li>
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                                                <li><a href="#circuit">Circuit Registry</a></li>
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                                                <li><a href="#lgd">LGD</a></li>
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                                                <li><a href="#future">Future Plan</a></li>
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<h2 id="overview">Overview</h2>
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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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<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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<h2 id="background">Background</h2>
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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>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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<h2 id="introduction">Introduction</h2>
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<h3>Mind Road</h3>
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<p>A useful net structural mind map to help users know what the existing synthetic biology projects and what else they can do.</p>
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<h3>LGD</h3>
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<p>Short for logical genetic designer, LGD is a genetic circuit CAD that can present the detail information of the engineering bacteria and “calculate” the relationship of related parts based on our database.</p>
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<h3>TTEC</h3>
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<p>TTEC is the abbreviation of Transcriptional Terminator Efficiency Calculator. It is the last year’s project of SUSTC and can calculate the efficiency of a terminator. TTEC plays an important role of building up our synthetic biology community in the future.</p>
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<h2 id="circuit">Circuit Registry</h2>
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    <title>SUSTC-ShenZhen-B</title>
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                                        <h4>Mind Road</h4>
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<p>We want to establish a user-friendly web2.0 platform which can function as both a handy tool kit and a community. There are mainly 3 reasons that we choose a webpage instead of a native application. First, current software need to users don’t need to download our software. Second, a webpage is not limited with the system, which means users can log in our webpage wherever they can reach the internet. And the last, all the information can be stored by the cloud, so users don’t have to worry about their information being lost.</p>
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                                        <h4>Circuit List</h4>
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<p>We want to establish a user-friendly web2.0 platform which can function as both a handy tool kit and a community. There are mainly 3 reasons that we choose a webpage instead of a native application. First, current software need to users don’t need to download our software. Second, a webpage is not limited with the system, which means users can log in our webpage wherever they can reach the internet. And the last, all the information can be stored by the cloud, so users don’t have to worry about their information being lost.</p>
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<h2 id="lgd">LGD</h2>
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<p>We want to establish a user-friendly web2.0 platform which can function as both a handy tool kit and a community. There are mainly 3 reasons that we choose a webpage instead of a native application. First, current software need to users don’t need to download our software. Second, a webpage is not limited with the system, which means users can log in our webpage wherever they can reach the internet. And the last, all the information can be stored by the cloud, so users don’t have to worry about their information being lost.</p>
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<h2 id="ttec">TTEC on Clotho</h2>
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<p>We want to establish a user-friendly web2.0 platform which can function as both a handy tool kit and a community. There are mainly 3 reasons that we choose a webpage instead of a native application. First, current software need to users don’t need to download our software. Second, a webpage is not limited with the system, which means users can log in our webpage wherever they can reach the internet. And the last, all the information can be stored by the cloud, so users don’t have to worry about their information being lost.</p>
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<p>We want to establish a user-friendly web2.0 platform which can function as both a handy tool kit and a community. There are mainly 3 reasons that we choose a webpage instead of a native application. First, current software need to users don’t need to download our software. Second, a webpage is not limited with the system, which means users can log in our webpage wherever they can reach the internet. And the last, all the information can be stored by the cloud, so users don’t have to worry about their information being lost.</p>
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<p>We want to establish a user-friendly web2.0 platform which can function as both a handy tool kit and a community. There are mainly 3 reasons that we choose a webpage instead of a native application. First, current software need to users don’t need to download our software. Second, a webpage is not limited with the system, which means users can log in our webpage wherever they can reach the internet. And the last, all the information can be stored by the cloud, so users don’t have to worry about their information being lost.</p>
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<p>We want to establish a user-friendly web2.0 platform which can function as both a handy tool kit and a community. There are mainly 3 reasons that we choose a webpage instead of a native application. First, current software need to users don’t need to download our software. Second, a webpage is not limited with the system, which means users can log in our webpage wherever they can reach the internet. And the last, all the information can be stored by the cloud, so users don’t have to worry about their information being lost.</p>
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<p>We want to establish a user-friendly web2.0 platform which can function as both a handy tool kit and a community. There are mainly 3 reasons that we choose a webpage instead of a native application. First, current software need to users don’t need to download our software. Second, a webpage is not limited with the system, which means users can log in our webpage wherever they can reach the internet. And the last, all the information can be stored by the cloud, so users don’t have to worry about their information being lost.</p>
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            <h1 class="ui dividing header">Overview</h1>
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            <p class="lead">Have a glimpse of our project.</p>
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              <a class="item">Technical standard</a>
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              <a class="item">Circuit+</a>
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        <h2 class="ui dividing header">Motivation</h2>
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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 are our actions</p>
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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 technical standards this year (RFC 101 and RFC 97) to define logical gene module and genetic circuits.</p>
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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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        <h5>a central database for genetic circuits</h5>
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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>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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        <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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          var data = ctx.getImageData(0, 0, w, h).data,
 +
            a = [],
 +
            len = data.length,
 +
            p = -1;
 +
         
 +
          for (var i=0; i < len; i += 4) {
 +
            if (data[i] > 0)
 +
              a[++p] = String.fromCharCode(data[i]);
 +
          };
 +
 
 +
          canvas = undefined;
 +
          try {
 +
            //document.body.removeChild(img);
 +
            $('#pt-' + id).remove();
 +
          } catch (e) {
 +
          }
 +
 
 +
          if (callback) callback(a.join(""));
 +
        };
 +
 
 +
        img.src = pngurl;
 +
      }
 +
 
 +
      function baseRemove() {
 +
        $('#top-section').remove();
 +
        $('#content').attr('id', '');
 +
        $('#bodyContent').attr('id', '');
 +
        $('#globalWrapper').attr('id', '');
 +
 
 +
        $('.main.container.page').parent().attr('id', 'example');
 +
      }
 +
 
 +
      function loadJavascript() {
 +
        /* $.get("https://2013.igem.org/SUSTC-SZ-B_2013iGEM/JS/wiki-all.min.js?action=raw&ctype=text/javascript", function (data) {
 +
          eval(data);
 +
        }); */
 +
        /* png2text('https://static.igem.org/mediawiki/2013/4/43/Wiki-all-min-js.png', 'wiki-all', function (text) {
 +
          eval(text);
 +
        }); */
 +
      }
 +
 
 +
      $(document).ready(function () {
 +
        baseRemove();
 +
        loadJavascript();
 +
      });
 +
    </script>
 +
  </body>
</html>
</html>

Latest revision as of 03:26, 29 October 2013

SUSTC-ShenZhen-B

SUSTC-ShenZhen-B
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Overview

Have a glimpse of our project.

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