|
|
| (24 intermediate revisions not shown) |
| Line 1: |
Line 1: |
| | + | {{:Team:Shenzhen BGIC 0101/Templates/Header}} |
| | <html> | | <html> |
| - | <head>
| + | <body> |
| - | <!-- iGem wiki hacks -->
| + | <br/> |
| - | <!-- Remove all empty <p> tags -->
| + | <h1>Overview：Genome Design Suite</h1> |
| - | <script type="text/javascript">
| + | |
| - | $(document).ready(function() {
| + | |
| - | $("p").filter( function() {
| + | |
| - | return $.trim($(this).html()) == '';
| + | |
| - | }).remove();
| + | |
| - | });
| + | |
| - | </script>
| + | |
| - | | + | |
| - | <!-- Remove "team" from the menubar -->
| + | |
| - | <script type="text/javascript">
| + | |
| - | $(document).ready(function() {
| + | |
| - | $("menubar > ul > li:last-child").remove();
| + | |
| - | });
| + | |
| - | </script>
| + | |
| - | | + | |
| - | <!-- Empty heading? - Then remove it.. -->
| + | |
| - | <script type="text/javascript">
| + | |
| - | $(document).ready(function() {
| + | |
| - | if ("" == "</html>{{{1}}}<html>") {
| + | |
| - | $("#heading").remove();
| + | |
| - | }
| + | |
| - | });
| + | |
| - | </script>
| + | |
| - | <script type="text/javascript">
| + | |
| - | $(document).ready(function() {
| + | |
| - | // document.getElementById("p-logo").style.display= "none";
| + | |
| - | document.getElementsByClassName("right-menu noprint")[0].style.display= "none";
| + | |
| - | //document.getElementById("searchform").style.display= "none";
| + | |
| - | | + | |
| - | });
| + | |
| - | </script>
| + | |
| - | | + | |
| - | <link rel="stylesheet" href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/css?action=raw&ctype=text/css" type="text/css" />
| + | |
| - | <link rel="stylesheet" href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/style?action=raw&ctype=text/css" type="text/css" />
| + | |
| - | <script src="http://code.jquery.com/jquery-1.7.2.min.js"></script>
| + | |
| - | <script type="text/javascript" src="https://2013.igem.org/Team:Shenzhen_BGIC_0101/easying?action=raw&ctype=text/javascript"></script>
| + | |
| - | <script type="text/javascript" src="//use.typekit.net/jlr8wlp.js"></script>
| + | |
| - | <script type="text/javascript">try{Typekit.load();}catch(e){}</script>
| + | |
| - | <script type="text/javascript">
| + | |
| - | function FloatMenu(){
| + | |
| - | var animationSpeed=1500;
| + | |
| - | var animationEasing='easeOutQuint';
| + | |
| - | var scrollAmount=$(document).scrollTop();
| + | |
| - | var newPosition=menuPosition+scrollAmount;
| + | |
| - | if($(window).height()<$('#fl_menu').height()+$('#fl_menu .menu').height()){
| + | |
| - | $('#fl_menu').css('top',menuPosition);
| + | |
| - | } else {
| + | |
| - | $('#fl_menu').stop().animate({top: newPosition}, animationSpeed, animationEasing);
| + | |
| - | }
| + | |
| - | }
| + | |
| - | $(window).load(function(){
| + | |
| - | menuPosition=$('#fl_menu').position().top;
| + | |
| - | FloatMenu();
| + | |
| - | });
| + | |
| - | $(window).scroll(function(){
| + | |
| - | FloatMenu();
| + | |
| - | });
| + | |
| - | $(document).ready(function(){
| + | |
| - | var fadeSpeed=500;
| + | |
| - | $("#fl_menu").hover(function(){
| + | |
| - | $('#fl_menu .label').fadeTo(fadeSpeed, 1);
| + | |
| - | $("#fl_menu .menu").fadeIn(fadeSpeed);
| + | |
| - | },function(){
| + | |
| - | $('#fl_menu .label').fadeTo(fadeSpeed, 0.75);
| + | |
| - | $("#fl_menu .menu").fadeOut(fadeSpeed);
| + | |
| - | });
| + | |
| - | });
| + | |
| - | </script>
| + | |
| - | <style>
| + | |
| - | | + | |
| - | .container{
| + | |
| - | width:65%;
| + | |
| - | left: 5%;
| + | |
| - | }
| + | |
| - | /* fl_menu */
| + | |
| - | #fl_menu{position:absolute;top:150px;left:-2px;z-index:9999;
| + | |
| - | width:200px;
| + | |
| - | height:50px;
| + | |
| - | }
| + | |
| - | #fl_menu .label{line-height:50px;font-size:18px;font-weight:bold;background: #1B1B1B;color:#fff;letter-spacing:5px;text-align: center;box-shadow: 2px 1px 6px #272727;border-radius: 2px;opacity: 0.75;}
| + | |
| - | #fl_menu .label a{color:#83f;text-decoration: none;}
| + | |
| - | #fl_menu .label a:hover{color:#38f;}
| + | |
| - | | + | |
| - | </style>
| + | |
| - | <!--[if lt IE 9]><script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script><![endif]-->
| + | |
| - | | + | |
| - | | + | |
| - | | + | |
| - | <style type="text/css">.recentcomments a{display:inline !important;padding:0 !important;margin:0 !important;}</style>
| + | |
| - | | + | |
| - | </head>
| + | |
| - | <body class="blog developer-wanted"> | + | |
| - | <div id="fl_menu"> | + | |
| - | <div class="label"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Software#">Overview</a></div>
| + | |
| - | <div class="label"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Modules">Modules</a></div> | + | |
| - | <div class="label"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Next_version">Next version</a></div>
| + | |
| - | <div class="label"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Compatibility">Compatibility</a></div>
| + | |
| - | <div class="label"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/NewStandard">New Standard</a></div>
| + | |
| - | <div class="label"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Tutorial">Tutorial</a></div>
| + | |
| - | <div class="label"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Web-based_trial">Web-based trial</a></div>
| + | |
| - | | + | |
| - | <div class="label"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Software_Assessment">Assessment</a></div>
| + | |
| - | <div class="label"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Downloadsl">Downloads</a></div>
| + | |
| - | | + | |
| - | | + | |
| - | </div>
| + | |
| - | <div id="wrap">
| + | |
| - | <header class="light">
| + | |
| - | <a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Home" id="logo">logo</a>
| + | |
| | | | |
| - | <nav class="menu-main-navigation-container"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Home" class="menu-item-20 menu-item menu-item-type-post_type menu-item-object-page">Home</a> <a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Team" class="menu-item-19 menu-item menu-item-type-post_type menu-item-object-page">Team</a> <a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Software" class="menu-item-18 menu-item menu-item-type-post_type menu-item-object-page current-menu-item">Software</a> <a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Requirements" class="menu-item-17 menu-item menu-item-type-post_type menu-item-object-page">Requirements</a> <a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Criteria" class="menu-item-15 menu-item menu-item-type-post_type menu-item-object-page">Criteria</a> </nav>
| + | <p>Genovo is a <b>Computer-Aided Design（CAD） suite</b> to assist users to create new system denovo.</p> |
| - | <a href="https://2013.igem.org/Main_Page" id="logo1">logo</a>
| + | <br/> |
| - | </header> | + | |
| | | | |
| - | | + | <p> |
| - | <div id="page-header" style="background: #cf9;height: 200px;box-shadow: 4px 3px 25px #cf9;"> | + | It sets us free in the laborious, complex creating procedure, including choosing genes of new system (here the system refers to new pathways which is in form of a chromosome), changing chromosome’s structure, editing coding DNA sequence, splitting the chromosome into equipped fragments for synthesis and assembly. |
| - | <h1 style="
| + | <br/><br/> |
| - | font-family: 'Tangerine', serif;
| + | Genovo’s UI is mainly developed on a genome browser, <a href="http://www.gmod.org/wiki/JBrowse">Jbrowse</a> interface<br/> |
| - | font-size: 5em;
| + | <img src="https://static.igem.org/mediawiki/2013/8/82/Genovoui.png" width=850px /> |
| - | text-shadow: 5px 6px 4px #467952;
| + | |
| - | color: #86E451;
| + | |
| - | letter-spacing: 0.2em;
| + | |
| - | word-spacing: 0.3em;
| + | |
| - | font-weight: 900;
| + | |
| - | line-height: 36px;
| + | |
| - | margin: 0;">Genovo</h1>
| + | |
| - | </div> | + | |
| | <br/> | | <br/> |
| - | <a name="overview"></a> | + | <br/><br/> |
| - | <section id="blog" class="container"> | + | Functionally, Genovo is partially based on <a href=" http://54.235.254.95/gd/"> GeneDesign</a> algorithm suite, and BioStudio development environment under < a href=" http://syntheticyeast.org/" >SC2.0 project</a>, but it has great extensions. |
| | + | </p> |
| | | | |
| - | <article class="clearfix" style="background: rgba(29, 28, 28, 0.79);">
| |
| - | <div id="post-1815" class="post-1815 post type-post status-publish format-standard hentry category-evolution" style="background: transparent;color: #E6E6E6;">
| |
| - | <div class="text">
| |
| - | <h2>Genovo</h2>
| |
| - |
| |
| - | <div class="post-content" style="color: #ADFFCF;"><hr/><p>
| |
| - | Genovo is a Computer-Aided Design（CAD） tool to create genome denovo.<br/><br/>
| |
| - | 1. operation interface<br/>
| |
| - | We developed its GUI & multiple functions basing upon JBrowse, a genome browse with a fully dynamic AJAX interface, which is included in GMOD in the CLOUD toolset.<br/>
| |
| - | <img src="https://static.igem.org/mediawiki/igem.org/d/d2/Jbrowse.png" /><img src="https://static.igem.org/mediawiki/igem.org/2/28/Gmod.png" /><br/>
| |
| - | 2. functional plugins<br/>
| |
| - | The current version is 1.3. It consists of 14 main plugins belonging to 3 design modules:<br/>
| |
| - | NeoChr, NecleoMod, SegmMan<br/><br/>
| |
| - | They are used to construct new chromosome structure denovo, modify CDS based on synoymous mutation, split chromosome into fragments with assembly adaptors in different sizes.<br/><br/>
| |
| - | The first module, NeoChr, would assist users to grab related genes in different pathways of various organism manually, to rewire genes’ relationship logically*, and to replace genes with orthologs that score higher*. Then it would allow users to define gene order and orientation in DRAG&DROP way, and decouple the genes with overlap. In the end, it would add or delete features, such as encrypted watermarks*, telomere, loxp sites to build a brand new genome.<br/><br/>
| |
| - | The second one , NucleoMod, has 5 applications. Firstly, NucleoMod is used to design CRISPR sites on NeoChr so that we can silence the wild type genes. Secondly, it can erase specific enzyme sites according to the users' selection. Thirdly, users can create a enzyme site in selected region of specific genes. Fourthly, it can optimize the codon efficiency to incresase the expression level. Finally, it can smash the tandem repeat bases to reduce the synthesis difficulty.<br/><br/>
| |
| - | The third one, SegmMan will cut chromosome into pieces in different sizes with Gibson, Goldengate, telomere adaptors to them so that they are able to be assembled into whole experimentally. Besides, it adds flanking vector homologous resion and enzyme sites for the preservation and excision from vectors.<br/><br/>
| |
| - | SegmMan, in another level, provide a complementary OLSDesign will guide users to get the chrosome fragments by chip and how to assembly them together.<br/><br/>
| |
| - | 3. software goals<br/><br/>
| |
| - | Genovo enables users to create chromosome-like biodevice denovo, from pathway guided selection of gene to the rewire of genes’ relation, from reasonable substitution of genes to alteration of genes’ location along chromosome addition, from modification to CDS sequence to automatically segmentation design globally for assembly.<br/><br/>
| |
| - | We hope Genovo would assist users to have their own designed chromosome even if in silico, and hope it would assist researchers in SC2.0 project and futher genome research in pathway level.<br/><br/>
| |
| - | <img src="https://static.igem.org/mediawiki/igem.org/f/f5/Sc.png" />
| |
| - |
| |
| - |
| |
| - |
| |
| - | </p>
| |
| | <br/><br/> | | <br/><br/> |
| - | </div> | + | <hr style="color:#7380AE; height:2px;" /> |
| - | </div>
| + | |
| - |
| + | |
| - | </div>
| + | |
| - |
| + | |
| - | </article>
| + | |
| - |
| + | |
| - | </section>
| + | |
| - | | + | |
| - | <div class="push"></div>
| + | |
| - | </div><!-- wrapper -->
| + | |
| - | <footer style>
| + | |
| - | <div class="container clearfix">
| + | |
| - | <div class="seven columns" id="footer-contact">
| + | |
| - | <h3>contact us</h3>
| + | |
| - | <p>BGI-Shenzhen, Beishan Industrial Zone<br />
| + | |
| - | Yantian District, Shenzhen, 518083, China</p>
| + | |
| - | <p> <span>email:</span><br />
| + | |
| - | <a href="mailto:gongjianhui@genomics.com">gongjianhui@genomics.com</a></p>
| + | |
| - | </div>
| + | |
| - | <div class="four columns" id="footer-project">
| + | |
| - | <h3>sponsor</h3>
| + | |
| - | <p>BGIC<br/></p>
| + | |
| - | </div>
| + | |
| - | <div class="five columns" id="footer-newsletter">
| + | |
| - | <a href="https://2013.igem.org/Main_Page" ><img width="150" height="120" src="https://static.igem.org/mediawiki/2013/0/02/TB_IGEM_official_logo.png" /></a>
| + | |
| - | </div>
| + | |
| - | </div>
| + | |
| - | </footer>
| + | |
| - | | + | |
| - | | + | |
| - | <script src="https://2013.igem.org/Team:Shenzhen_BGIC_0101/aaa?action=raw&ctype=text/javascript"></script>
| + | |
| | | | |
| | | | |
| | </body> | | </body> |
| | </html> | | </html> |
It sets us free in the laborious, complex creating procedure, including choosing genes of new system (here the system refers to new pathways which is in form of a chromosome), changing chromosome’s structure, editing coding DNA sequence, splitting the chromosome into equipped fragments for synthesis and assembly.
Genovo’s UI is mainly developed on a genome browser, Jbrowse interface
Functionally, Genovo is partially based on GeneDesign algorithm suite, and BioStudio development environment under SC2.0 project, but it has great extensions.
"
