Difference between revisions of "Team:SJTU-software/Design"

(Prototype team page)
 
 
(20 intermediate revisions by 2 users not shown)
Line 1: Line 1:
 
{{SJTU-software}}
 
{{SJTU-software}}
 
<html>
 
<html>
 +
<style>
 +
            /*================================================================================*/
 +
            /*public engagement*/
 +
            #posts-list {
 +
                position: relative;
 +
                width: 720px;
 +
                margin-top: 15px;
 +
                margin-left: 30px;
 +
                margin-bottom: 40px;
 +
                float: left;
 +
            }
  
−
<div class="column full_size">
+
            #posts-list article {
−
<h1>Design</h1>
+
            position: relative;
−
<p>
+
            margin-bottom: 40px;
−
Design is the first step in the design-build-test cycle in engineering and synthetic biology. Use this page to describe the process that you used in the design of your parts. You should clearly explain the engineering principles used to design your project.
+
            padding-bottom: 40px;
−
</p>
+
            border-bottom: 1px solid #6b3b25;
 +
            text-align:justify;
 +
            }
 +
            #posts-list article:last-child {
 +
            border: none;
 +
            }
 +
            #posts-list article .feature-image {
 +
            position: relative;
 +
            line-height: 0px;
 +
            border: 5px solid #fff;
 +
            -webkit-box-shadow: 0px 0px 5px rgba(0, 0, 0, 0.2);
 +
            -moz-box-shadow: 0px 0px 5px rgba(0, 0, 0, 0.2);
 +
            -o-box-shadow: 0px 0px 5px rgba(0, 0, 0, 0.2);
 +
            box-shadow: 0px 0px 5px rgba(0, 0, 0, 0.2);
 +
            margin: 0px 66px 6px 66px;
 +
            }
 +
            #posts-list article .feature-image:after {
 +
            position: absolute;
 +
            bottom: -22px;
 +
            left: 0px;
 +
            content: '';
 +
            background: url(https://static.igem.org/mediawiki/2018/2/2e/T--SJTU-software--stacked-paper.png) no-repeat right bottom;
 +
            width: 100%;
 +
            height: 17px;
 +
            }
 +
            #posts-list article .feature-image img {
 +
            max-width: 100%;
 +
            }
 +
            #posts-list article .meta {
 +
            color: #c78301;
 +
            text-shadow: 0px 1px 0 rgba(255, 255, 255, 0.5);
 +
            font-family: "HelveticaNeue", "Helvetica Neue", Helvetica, Arial, serif;
 +
            font-size: 18px;
 +
            margin-bottom: 14px;
 +
            }
 +
            #posts-list article .meta a {
 +
            color: #c78301;
 +
            text-decoration: none;
 +
            }
 +
            #posts-list article .entry-title {
 +
            color: #6b3b25;
 +
            text-shadow: 0px 1px 0 rgba(255, 255, 255, 0.5);
 +
            margin-bottom: 14px;
 +
            }
 +
            #posts-list article .entry-title .post-heading {
 +
            color: #6b3b25;
 +
            text-decoration: none;
 +
            font-family: "HelveticaNeue", "Helvetica Neue", Helvetica, Arial, sans-serif;
 +
            font-size: 24px;
 +
            font-weight: 700;
 +
            }
 +
            #posts-list article .subtitle{
 +
                color: #6b3b25;
 +
                text-decoration: none;
 +
                font-family: "HelveticaNeue", "Helvetica Neue", Helvetica, Arial, sans-serif;
 +
                font-size: 20px;
 +
                font-weight: 600;
 +
            }
 +
            #posts-list article .excerpt {
 +
            text-shadow: 0px 1px 0 rgba(255, 255, 255, 0.5);
 +
            margin-bottom: 21px;
 +
            font-family: "HelveticaNeue", "Helvetica Neue", Helvetica, Arial, serif;
 +
            font-size: 18px;
 +
            line-height: 1.5em;
 +
            color: #6b3b25;
 +
            }
 +
            #posts-list.single-post article {
 +
            border: none;
 +
            }
 +
            /*-----------------------------------------------------------------------------------*/
 +
            /* PAGE NAVIGATION
 +
            /*-----------------------------------------------------------------------------------*/
 +
            #posts-list .page-navigation {
 +
            position: relative;
 +
            left: 50%;
 +
            display: block;
 +
            margin-bottom: 100px;
 +
            float: left;
 +
            }
 +
            #posts-list .page-navigation div {
 +
            position: relative;
 +
            right: 50%;
 +
            }
 +
            #posts-list .page-navigation div span {
 +
            margin-bottom: 15px;
 +
            display: inline-block;
 +
            }
 +
            #posts-list .page-navigation div:hover a {
 +
            color: #6b3b25;
 +
            }
 +
            #posts-list .page-navigation a {
 +
            -webkit-transition: all 0.3s ease;
 +
            -moz-transition: all 0.3s ease;
 +
            -o-transition: all 0.3s ease;
 +
            transition: all 0.3s ease;
 +
            color: #fff;
 +
            display: block;
 +
            font-size: 12px;
 +
            line-height: 41px;
 +
            width: 112px;
 +
            text-decoration: none;
 +
            text-align: center;
 +
            }
 +
            #posts-list .page-navigation .nav-next {
 +
            float: left;
 +
            margin-right: 20px;
 +
            background: url(https://static.igem.org/mediawiki/2018/2/2d/T--SJTU-software--pagination.png) no-repeat 0px 0px;
 +
            }
 +
            #posts-list .page-navigation .nav-previous {
 +
            float: right;
 +
            background: url(https://static.igem.org/mediawiki/2018/2/2d/T--SJTU-software--pagination.png) no-repeat right -59px;
 +
            }
 +
            /*-----------------------------------------------------------------------------------*/
 +
    /*-----------------------------------------------------------------------------------*/
 +
    /* SIDEBAR
 +
    /*-----------------------------------------------------------------------------------*/
 +
    #sidebar {
 +
    position: relative;
 +
    width: 220px;
 +
    margin-right: 30px;
 +
    margin-top: 30px;
 +
    margin-bottom: 30px;
 +
    float: right;
 +
    }
 +
    #sidebar .block {
 +
    font-size: 17px;
 +
    margin-bottom: 15px;
 +
    font-family: "HelveticaNeue", "Helvetica Neue", Helvetica, Arial, sans-serif;
 +
    text-shadow: 0px 1px 0 rgba(255, 255, 255, 0.5);
 +
    }
 +
    #sidebar .block a {
 +
    text-decoration: none;
 +
    color: #c78301;
 +
    }
 +
    #sidebar .block a:hover {
 +
    border-bottom: 1px dotted #c78301;
 +
    }
 +
    #sidebar .block .heading {
 +
    color: #6b3b25;
 +
    font-family: "HelveticaNeue", "Helvetica Neue", Helvetica, Arial, sans-serif;
 +
    font-weight: 700;
 +
    line-height: 20px;
 +
    font-size: 20px;
 +
    border-top: 4px solid #6b3b25;
 +
    border-bottom: 1px solid #6b3b25;
 +
    text-shadow: 0px 1px 0 rgba(255, 255, 255, 0.5);
 +
    margin-top: 0px;
 +
    }
 +
    #sidebar .ads img {
 +
    margin-bottom: 10px;
 +
    margin-right: 0px;
 +
    }
 +
    /*-----------------------------------------------------------------------------------*/
  
−
<p>
+
            .headline{
−
This page is different to the "Applied Design Award" page. Please see the <a href="https://2018.igem.org/Team:SJTU-software/Applied_Design">Applied Design</a> page for more information on how to compete for that award.
+
                color: #6b3b25;
−
</p>
+
                text-decoration: none;
 +
                font-family: "HelveticaNeue", "Helvetica Neue", Helvetica, Arial, sans-serif;
 +
                font-size: 32px;
 +
                font-weight: 800;
 +
                margin: 20px;
 +
            }
 +
            ul{
 +
                list-style:none;
 +
            }
  
−
</div>
+
            li{
 +
      padding: 4px 0px 1px 0px;
 +
      margin: 2px 0px 1px 0px;
 +
    }
 +
</style>
  
  
 +
<body>
 +
    <div class="wrapper">
  
−
<div class="column two_thirds_size">
+
        <!-- MAIN-->
−
<h3>What should this page contain?</h3>
+
            <div id="main" class="cf">
−
<ul>
+
                <div class="headline">
−
<li>Explanation of the engineering principles your team used in your design</li>
+
                    Project —— Design & Contribution
−
<li>Discussion of the design iterations your team went through</li>
+
                </div>
−
<li>Experimental plan to test your designs</li>
+
                    <!-- posts list -->
−
</ul>
+
                    <div id="posts-list" class="cf">  
 +
                       
 +
                        <article class="cf" id="Design" >
 +
                            <div class="entry-title">
 +
                                <div class="post-heading" >Design</div>
 +
                            </div>
 +
                            <div class="excerpt">
 +
                                Since the birth of synthetic biology in 2000, metabolic engineering has made increasingly huge progress on high value-added natural products. The synthesis and construction of metabolic pathways play a fundamental role in microbiology, biochemistry, and many other relevant fields. In 2003, Jay Keasling’s team reconstructed the biological synthesis pathway of arteannuinic acid in E. coli, providing functional confirmation for this metabolic process. In recent years, researchers have engineered yeast to produce a variety of plant-based natural products. These pathways are likely to involve the introduction of many heterologous genes and numerous genetic modifications to increase productivity. In the biosynthesis of opioids in yeast, 17 enzymes from different plants, animals, and yeasts were encoded through synthetic biological way. Although there are several tools for scientists to analyze and select the potential genes of the designed pathway, these tools all focus on the one or two specific gene instead of the whole metabolic system. Therefore, what our team’s trying to do is making comparisons between the designed pathway we want to synthesize and the natural-existing pathways to make sure that the researchers can get the whole picture. In this way, scientists can learn more about molecular functions and biological process from an innovating aspect.
 +
                            </div>
 +
                       
 +
                            <div class="excerpt">
 +
                              During the project, we had the pleasure to interview a PhD student in the university of Toronto. Based on his experiences working on biological metabolism, changing from several different software to visualize the network, do simulations or other studies, is quite inconvenient. Therefore, he suggested us to make our tool more handful for researches by integrating a few frequently-used functions together.
 +
                            </div>
  
−
</div>
+
                          <div class="excerpt">                           
 +
                            Besides, according to our survey among students in the biology department in our school, an integrated synthetic biology tool box was in urgent need. So we selected some commonly-needed functions to combine into the toolkit, containing SBML Drawer, SBML Differ, SMILES Drawer and DNA Editor. We found these existing open-source projects, did some modification and improvement, and integrated them into our Metlab.  
 +
                            </div>
  
−
<div class="column third_size">
+
                            <div class="excerpt">                            
−
<div class="highlight decoration_A_full">
+
Now, we are still conducting more user surveys and looking for more practical needs. For these user demands, we will seek existing projects or develop more softwares, making our tool box more integrated.
−
<h3>Inspiration</h3>
+
                            </div>
−
<ul>
+
                             
−
<li><a href="https://2016.igem.org/Team:MIT/Experiments/Promoters">2016 MIT</a></li>
+
                        </article>
−
<li><a href="https://2016.igem.org/Team:BostonU/Proof">2016 BostonU</a></li>
+
−
<li><a href="https://2016.igem.org/Team:NCTU_Formosa/Design">2016 NCTU Formosa</a></li>
+
−
</ul>
+
−
</div>
+
−
</div>
+
  
 +
                        <article class="cf" id="Contribution">
 +
                            <div class="entry-title">
 +
                                <div class="post-heading"  >Contribution</div>
 +
                            </div>
 +
                            <div class="excerpt">
 +
                                The aim of our project has always been designing and developing useful programs for Synthetic Biology and iGEM community. Comparative analysis of biological network is very useful and indicative in synthetic biology and other related studies. Specially, it enables people to handle unknown organisms starting from known ones with alike networks. However, most current tools are only for a specific problem or application, and the existing algorithm is inefficient. In order to solve these problems, we launch METLAB, a general purpose alignment software.
 +
                            </div>
 +
                       
 +
                            <div class="excerpt">
 +
                              Metlab is a suite of synthetic biology aided tools and mainly functions as BLAST for networks. Besides network alignment, users may visualize networks, compare and draw metabolites and design their wet-lab experiments.
 +
                            </div>
  
 +
                          <div class="excerpt">
 +
                              Combining various commonly-used functions into the toolkit, our project will definitely come in handy to people studying synthetic biology and related fields.
 +
                            </div>
 +
                           
 +
                        </article>                                     
 +
            </div>
 +
 +
  <!-- SIDEBAR -->
 +
                    <aside id="sidebar" >
 +
                   
 +
                        <ul>
 +
                            <li class="block">
 +
                                <h4 class="heading" align="center">Design & Contribution</h4>
 +
                                <ul>
 +
                                    <li class="cat-item"><a href="#Design" >Design</a></li>
 +
                                    <li class="cat-item"><a href="#Contribution" >Contribution</a></li>
 +
                                 
 +
                                </ul>
 +
                            </li>
 +
                        </ul>
 +
                    </aside>
 +
                    <!-- ENDS SIDEBAR -->
 +
                   
 +
                </div>
 +
 +
        <!-- ENDS MAIN -->
 +
</body>
  
 
</html>
 
</html>
 +
{{SJTU-software/Widget}}

Latest revision as of 08:07, 17 October 2018

SJTU-software
Metlab: a metabolic network research tool box
Project —— Design & Contribution
Design
Since the birth of synthetic biology in 2000, metabolic engineering has made increasingly huge progress on high value-added natural products. The synthesis and construction of metabolic pathways play a fundamental role in microbiology, biochemistry, and many other relevant fields. In 2003, Jay Keasling’s team reconstructed the biological synthesis pathway of arteannuinic acid in E. coli, providing functional confirmation for this metabolic process. In recent years, researchers have engineered yeast to produce a variety of plant-based natural products. These pathways are likely to involve the introduction of many heterologous genes and numerous genetic modifications to increase productivity. In the biosynthesis of opioids in yeast, 17 enzymes from different plants, animals, and yeasts were encoded through synthetic biological way. Although there are several tools for scientists to analyze and select the potential genes of the designed pathway, these tools all focus on the one or two specific gene instead of the whole metabolic system. Therefore, what our team’s trying to do is making comparisons between the designed pathway we want to synthesize and the natural-existing pathways to make sure that the researchers can get the whole picture. In this way, scientists can learn more about molecular functions and biological process from an innovating aspect.
During the project, we had the pleasure to interview a PhD student in the university of Toronto. Based on his experiences working on biological metabolism, changing from several different software to visualize the network, do simulations or other studies, is quite inconvenient. Therefore, he suggested us to make our tool more handful for researches by integrating a few frequently-used functions together.
Besides, according to our survey among students in the biology department in our school, an integrated synthetic biology tool box was in urgent need. So we selected some commonly-needed functions to combine into the toolkit, containing SBML Drawer, SBML Differ, SMILES Drawer and DNA Editor. We found these existing open-source projects, did some modification and improvement, and integrated them into our Metlab.  
Now, we are still conducting more user surveys and looking for more practical needs. For these user demands, we will seek existing projects or develop more softwares, making our tool box more integrated.
Contribution
The aim of our project has always been designing and developing useful programs for Synthetic Biology and iGEM community. Comparative analysis of biological network is very useful and indicative in synthetic biology and other related studies. Specially, it enables people to handle unknown organisms starting from known ones with alike networks. However, most current tools are only for a specific problem or application, and the existing algorithm is inefficient. In order to solve these problems, we launch METLAB, a general purpose alignment software.
Metlab is a suite of synthetic biology aided tools and mainly functions as BLAST for networks. Besides network alignment, users may visualize networks, compare and draw metabolites and design their wet-lab experiments.
Combining various commonly-used functions into the toolkit, our project will definitely come in handy to people studying synthetic biology and related fields.

    Address

    NO. 800 Dongchuan Road, Minhang District, Shanghai, China

    Contact Us

    rockywei@sjtu.edu.cn

    SJTU-software