Team:SYSU-Software

From 2012.igem.org

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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml">
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<head>
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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<title>HomeHTML/CSSJavaScriptResourcesT</title>
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<link rel="stylesheet" href="style.css" />
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<link href="examples.css" rel="stylesheet" />
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<link href="style/carousel.css" rel="stylesheet" />
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<link href="layout.css" rel="stylesheet" type="text/css" />
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<script src="js/ext-core-debug.js"></script>
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<script src="js/carousel.js"></script>
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<script>
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            Ext.onReady(function() {
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                new Ext.ux.Carousel('simple-example');
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                new Ext.ux.Carousel('full-example', {
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                    itemSelector: 'img',
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                    interval: 3,
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                    autoPlay: true,
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                    showPlayButton: true,
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                    pauseOnNavigate: true,
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                    freezeOnHover: true,
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                    transitionType: 'fade',
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                    navigationOnHover: true     
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                });
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                new Ext.ux.Carousel('html-example', {
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                    itemSelector: 'div.item',
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                    interval: 5,
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                    autoPlay: true,
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                    transitionEasing: 'easeIn'               
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                });
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            })
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        </script>
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        <!-- ----------------------------------------------------- -->
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<style type="text/css">
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body{background: url('bg.png') repeat scroll 0 0 #FEFEFE;}
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a {
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color: #808080;
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font-size: 9pt;
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text-decoration: none;
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}
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a:hover { color: white; }
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.blk_18 { overflow:hidden; zoom:1; font-size:9pt; border:1px solid #e3e3e3; background:#eee; width:692px; margin-top:8px; }
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.blk_18 .pcont { width:638px; float:left; overflow:hidden; padding-left:5px; }
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.blk_18 .ScrCont { width:32766px; zoom:1; margin-left:-5px; }
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.blk_18 #List1_1, .blk_18 #List2_1 { float:left; }
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.blk_18 .LeftBotton, .blk_18 .RightBotton { width:15px; height:74px; float:left; background:url(ax.gif) no-repeat; }
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.blk_18 .LeftBotton { background-position: 0 0; margin:8px 5px 0; }
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.blk_18 .RightBotton { background-position: 0 -100px; margin:8px 1px 10px 5px; }
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.blk_18 .LeftBotton:hover { background-position: -20px 0; }
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.blk_18 .RightBotton:hover { background-position: -20px -100px; }
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.blk_18 .pl img { display:block; cursor:pointer; border:none; margin:6px auto 1px auto; }
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.blk_18 .pl { width:105px; border:1px solid #f3f3f3; float:left; float:left; text-align:center; line-height:24px; }
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.blk_18 a.pl:hover { border:1px solid #5dacec; color:#5dacec; background:#fff; }
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</style>
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<script type="text/javascript">
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var Speed_1 = 10; //速度(毫秒)
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var Space_1 = 20; //每次移动(px)
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var PageWidth_1 = 107 * 6; //翻页宽度
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var interval_1 = 5000; //翻页间隔时间
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var fill_1 = 0; //整体移位
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var MoveLock_1 = false;
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var MoveTimeObj_1;
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var MoveWay_1="right";
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var Comp_1 = 0;
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var AutoPlayObj_1=null;
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function GetObj(objName){if(document.getElementById){return eval('document.getElementById("'+objName+'")')}else{return eval('document.all.'+objName)}}
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function AutoPlay_1(){clearInterval(AutoPlayObj_1);AutoPlayObj_1=setInterval('ISL_GoDown_1();ISL_StopDown_1();',interval_1)}
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function ISL_GoUp_1(){if(MoveLock_1)return;clearInterval(AutoPlayObj_1);MoveLock_1=true;MoveWay_1="left";MoveTimeObj_1=setInterval('ISL_ScrUp_1();',Speed_1);}
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function ISL_StopUp_1(){if(MoveWay_1 == "right"){return};clearInterval(MoveTimeObj_1);if((GetObj('ISL_Cont_1').scrollLeft-fill_1)%PageWidth_1!=0){Comp_1=fill_1-(GetObj('ISL_Cont_1').scrollLeft%PageWidth_1);CompScr_1()}else{MoveLock_1=false}
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AutoPlay_1()}
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function ISL_ScrUp_1(){if(GetObj('ISL_Cont_1').scrollLeft<=0){GetObj('ISL_Cont_1').scrollLeft=GetObj('ISL_Cont_1').scrollLeft+GetObj('List1_1').offsetWidth}
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GetObj('ISL_Cont_1').scrollLeft-=Space_1}
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function ISL_GoDown_1(){clearInterval(MoveTimeObj_1);if(MoveLock_1)return;clearInterval(AutoPlayObj_1);MoveLock_1=true;MoveWay_1="right";ISL_ScrDown_1();MoveTimeObj_1=setInterval('ISL_ScrDown_1()',Speed_1)}
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function ISL_StopDown_1(){if(MoveWay_1 == "left"){return};clearInterval(MoveTimeObj_1);if(GetObj('ISL_Cont_1').scrollLeft%PageWidth_1-(fill_1>=0?fill_1:fill_1+1)!=0){Comp_1=PageWidth_1-GetObj('ISL_Cont_1').scrollLeft%PageWidth_1+fill_1;CompScr_1()}else{MoveLock_1=false}
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AutoPlay_1()}
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function ISL_ScrDown_1(){if(GetObj('ISL_Cont_1').scrollLeft>=GetObj('List1_1').scrollWidth){GetObj('ISL_Cont_1').scrollLeft=GetObj('ISL_Cont_1').scrollLeft-GetObj('List1_1').scrollWidth}
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GetObj('ISL_Cont_1').scrollLeft+=Space_1}
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function CompScr_1(){if(Comp_1==0){MoveLock_1=false;return}
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var num,TempSpeed=Speed_1,TempSpace=Space_1;if(Math.abs(Comp_1)<PageWidth_1/2){TempSpace=Math.round(Math.abs(Comp_1/Space_1));if(TempSpace<1){TempSpace=1}}
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if(Comp_1<0){if(Comp_1<-TempSpace){Comp_1+=TempSpace;num=TempSpace}else{num=-Comp_1;Comp_1=0}
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GetObj('ISL_Cont_1').scrollLeft-=num;setTimeout('CompScr_1()',TempSpeed)}else{if(Comp_1>TempSpace){Comp_1-=TempSpace;num=TempSpace}else{num=Comp_1;Comp_1=0}
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GetObj('ISL_Cont_1').scrollLeft+=num;setTimeout('CompScr_1()',TempSpeed)}}
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function picrun_ini(){
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GetObj("List2_1").innerHTML=GetObj("List1_1").innerHTML;
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GetObj('ISL_Cont_1').scrollLeft=fill_1>=0?fill_1:GetObj('List1_1').scrollWidth-Math.abs(fill_1);
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GetObj("ISL_Cont_1").onmouseover=function(){clearInterval(AutoPlayObj_1)}
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GetObj("ISL_Cont_1").onmouseout=function(){AutoPlay_1()}
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AutoPlay_1();
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}
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</script>
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 +
<style>
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.menu {
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height: 45px;
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display: block;
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}
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.menu ul {
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list-style: none;
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padding: 0;
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margin: 0;
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}
 +
 +
.menu ul li {
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float: left;
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/* 菜单子元素的内容超出不可见 */ 
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overflow: hidden;
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position: relative;
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text-align: center;
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line-height: 45px;
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}
 +
 +
.menu ul li a {
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/* 必须是相对定位  */
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position: relative;
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display: block;
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width: 110px;
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height: 45px;
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font-family: Arial;
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font-size: 11px;
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font-weight: bold;
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letter-spacing: 1px;
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text-transform: uppercase;
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text-decoration: none;
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cursor: pointer;
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}
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.menu ul li a span {
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/* 所有层将使用绝对定位 */
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position: absolute;
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left: 0;
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width: 110px;
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}
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.menu ul li a span.out {
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top: 0px;
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}
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.menu ul li a span.over,
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.menu ul li a span.bg {
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/* 起初.over层和.bg层相对a元素-45px以达到隐藏 */ 
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top: -45px;
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}
 +
 +
/** 完整版示例 **/
 +
 +
#menu {
 +
background:url(bg_menu.gif) scroll 0 -1px repeat-x;
 +
border:1px solid #CCC;
 +
}
 +
 +
#menu ul li a {
 +
color: #000;
 +
}
 +
 +
#menu ul li a span.over {
 +
color: #FFF;
 +
}
 +
 +
#menu ul li span.bg {
 +
height: 45px;
 +
background: url(bg_over.gif) center center no-repeat;
 +
}
 +
 +
/** 简化版示例 **/
 +
 +
#menu2 {
 +
background: #000000;
 +
}
 +
 +
#menu2 ul li a {
 +
color:#FFF;
 +
}
 +
 +
#menu2 ul li a span.over {
 +
background: #A6DD00;
 +
color:#333;
 +
}
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#menu2 ul li.nav1 a span.over {
 +
background: #fea274;
 +
}
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#menu2 ul li.nav2 a span.over {
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background: #b0bbba;
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}
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#menu2 ul li.nav3 a span.over {
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background: #a3f091;
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}
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#menu2 ul li.nav4 a span.over {
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background: #86dbf9;
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}
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#menu2 ul li.nav5 a span.over {
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background: #e0caf0;
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}
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#menu2 ul li.nav6 a span.over {
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background: #9dace9;
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}
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 +
.style1 {
 +
color: #FFFFFF;
 +
}
 +
 +
 +
 +
</style>
 +
<script type="text/javascript" src="jquery.min.js"></script>
 +
<script language="javascript">
 +
$(document).ready(function() {
 +
 +
/* 完整版示例 */
 +
 +
// 把每个a中的内容包含到一个层（span.out）中，在span.out层后面追加背景图层（span.bg）
 +
$("#menu li a").wrapInner( '<span class="out"></span>' ).append( '<span class="bg"></span>' );
 +
 +
// 循环为菜单的a每个添加一个层（span.over）
 +
$("#menu li a").each(function() {
 +
$( '<span class="over">' +  $(this).text() + '</span>' ).appendTo( this );
 +
});
 +
 +
$("#menu li a").hover(function() {
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// 鼠标经过时候被触发的函数
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$(".out",this).stop().animate({'top':'45px'},250); // 向下滑动 - 隐藏
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$(".over",this).stop().animate({'top':'0px'},250); // 向下滑动 - 显示
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$(".bg",this).stop().animate({'top':'0px'}, 120); // 向下滑动 - 显示
 +
 +
}, function() {
 +
// 鼠标移出时候被触发的函数
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$(".out",this).stop().animate({'top':'0px'},250); // 向上滑动 - 显示
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$(".over",this).stop().animate({'top':'-45px'},250); // 向上滑动 - 隐藏
 +
$(".bg",this).stop().animate({'top':'-45px'},120); // 向上滑动 - 隐藏
 +
});
 +
 +
 +
/* 简化版示例 */
 +
 +
$("#menu2 li a").wrapInner( '<span class="out"></span>' );
 +
 +
$("#menu2 li a").each(function() {
 +
$('<span class="over">' +  $(this).text() + '</span>' ).appendTo( this );
 +
});
 +
 +
$("#menu2 li a").hover(function() {
 +
$(".out",this).stop().animate({'top':'45px'},200); // 向下滑动 - 隐藏
 +
$(".over",this).stop().animate({'top':'0px'},200); // 向下滑动 - 显示
 +
 +
}, function() {
 +
$(".out",this).stop().animate({'top':'0px'},200); // 向上滑动 - 显示
 +
$(".over",this).stop().animate({'top':'-45px'},200); // 向上滑动 - 隐藏
 +
});
 +
 +
});
 +
 +
</script>
 +
<!-- ----------------------------------------------------------------------------------- -->
 +
<style  type="text/css">
 +
 +
 +
 +
 +
 +
.projecttext {
 +
font-family: "Times New Roman", Times, serif;
 +
font-size: large;  padding: 8px;
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}
 +
.style2 {
 +
font-family: "Times New Roman", Times, serif;
 +
font-size: x-large;
 +
}
 +
 +
 +
 +
 +
 +
.softwaretext {
 +
font-family: "Times New Roman", Times, serif;
 +
font-size: large;
 +
}
 +
 +
 +
 +
 +
 +
</style>
 +
<!-- ----------------------------------------------------------------------------------- -->
 +
<link href="stylesoftware.css" rel="stylesheet" type="text/css" />
 +
<script type="text/javascript" src="jquery-latest.pack.js"></script>
 +
<script type="text/javascript">
 +
function loadnext(divout,divin){
 +
 +
$("." + divout).hide();
 +
$("." + divin).fadeIn("fast");
 +
}
 +
 +
 +
 +
</script>
 +
<!-- ----------------------------------------------------------------------------------- -->
 +
 +
 +
 +
</head>
 +
 +
<body onload="new Accordian('basic-accordian',5,'header_highlight');">
 +
 +
<div id="content">
 +
 +
<div id="menu2" class="menu">
 +
<ul>
 +
<li class="nav1"><a href="javascript:;" >Home</a></li>
 +
<li class="nav2"><a href="javascript:;">Project</a></li>
 +
<li class="nav3"><a href="javascript:;">Software</a></li>
 +
                <li class="nav4"><a href="javascript:;">Extra</a></li>
 +
<li class="nav5"><a href="javascript:;">Team</a></li>
 +
<li class="nav6"><a href="javascript:;">About</a></li>
 +
</ul>
 +
</div><h3>Project</h3>
 +
</div>
 +
<!-- ----------------------------------------------------------------------------------- -->
 +
<div style="margin:auto;width:980px;height: 364px; background:#b0bbba;"><div style="position: absolute;width:420px;height: 120px;"><p class="projecttext">
 +
<span class="style2">W</span><span >e have inclination to
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develop a multifunctional toolbox “Blablabla”, that integrates different
 +
modules together and help researchers approach information they need.</span></p>
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</div>
 +
<img alt="" style="position: absolute; margin-top:110px;  top: 115px;"; src=  ssss.png width="400" height="132" />
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 +
<img  src= 搜狗截图_2012-07-05_12-53-06.png style="  position: absolute ; margin-left:420px;" width="565" height="364" />
 +
 +
<img  style="position: absolute;top: 350px;  margin-left: 90px;"src=  782d390aae3c898ea8db9493cb53c3e0.png width="234" height="100" />
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</div>
 +
 +
 +
<!-- ----------------------------------------------------------------------------------- -->
 +
<div style="margin:auto;width:980px;  height: 500px; position:  static">
 +
<h3>SOFTWARE </h3>
 +
<div id="wizardwrapper">
 +
 +
  <div class="1">
 +
 +
    <h4>Genome Viewer</h4>
 +
    <div id="wizardcontent" class="softwaretext"><p> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Firstly, we consider the Genome Viewer, which visualizes the E coli genome, locates the genes on the genome and make it easy to study the characteristics of the genome.</p><p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;With this Genome Browser, researchers can approach most information on biotechnology. Users are able to search Biobricks, plasmids and genomes of model microorganisms, in the same time, gene annotations and information of GenBank are presented. The protein sequence is also showed according to the DNA sequences. Aside from searching sequences, users can also input or modify the sequences, insert annotation and build target plasmids they need. The Genome Browser support the format of FASTA  when import and export the sequences.</p></div>
 +
    <div class="buttons">
 +
      <button type="submit" class="previous"  disabled="disabled"> <img src="images/arrow_left.png" alt=""/> Back </button>
 +
      <button type="submit" class="next" onclick="loadnext(1,2);"> Next <img src="images/arrow_right.png" alt="" /> </button>
 +
 +
    </div>
 +
    <ul id="mainNav" class="fiveStep">
 +
      <li class="current"><a title=""><em>Part 1: Genome Viewer</em></a></li>
 +
      <li><a title=""><em>Part 2: Database</em></a></li>
 +
      <li><a title=""><em>Part 3: Riboswitch Designer</em></a></li>
 +
      <li><a title=""><em>Part 4: Network Illustrator</em></a></li>
 +
 +
      <li class="mainNavNoBg"><a title=""><em>Part 5: Simulator</em> </a></li>
 +
    </ul>
 +
    <div style="clear:both"></div>
 +
  </div>
 +
 +
  <div id="wizardpanel" class="2">
 +
    <h4>Database</h4>
 +
    <div id="wizardcontent" class="softwaretext"><p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Secondly, to meet the need of protein-protein interaction researches, we optimize the methods of scanning and output of the existing database, and also supplement the biological information by building novel database. </p><p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This part of the software focus on the design of regulatory elements of metabolic networks, mainly non-coding RNAs including SiRNA and Riboswitch. When a certain gene or protein is given, the Designer would generate the elements. What’s more, the primary and secondary structure can be predicted and presented in the Designer. The function of structure prediction can be also applied in other non-coding RNAs, for instance, microRNAs.</p></div>
 +
 +
    <div class="buttons">
 +
      <button type="submit" class="previous" onclick="loadnext(2,1);"> <img src="images/arrow_left.png" alt="" /> Back </button>
 +
      <button type="submit" class="next" onclick="loadnext(2,3);"> Next <img src="images/arrow_right.png" alt="" /> </button>
 +
    </div>
 +
    <ul id="mainNav" class="fiveStep">
 +
      <li class="lastDone"><a href="/" title=""><em>Part 1: Genome Viewer</em></a></li>
 +
 +
      <li class="current"><a title=""><em>Part 2: Database</em></a></li>
 +
      <li><a title=""><em>Part 3: Riboswitch Designer</em></a></li>
 +
      <li><a title=""><em>Part 4: Network Illustrator</em></a></li>
 +
      <li class="mainNavNoBg"><a title=""><em>Part 5: Simulator</em> </a></li>
 +
 +
    </ul><div style="clear:both"></div>
 +
  </div>
 +
 
 +
 
 +
  <div id="wizardpanel" class="3">
 +
    <h4>Riboswitch Designer</h4>
 +
    <div id="wizardcontent" class="softwaretext"><p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Thirdly, we develop a Riboswitch Designer, to help the design of riboswitch, a thriving method applied in biological research, by building an optimized algorithm.</p><p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Relying on the KEGG Pathway database, the Illustrator exports the optimized relevant pathway map of a gene or transcription factor the user interests in. </p> </div>
 +
    <div class="buttons">
 +
      <button type="submit" class="previous" onclick="loadnext(3,2);"> <img src="images/arrow_left.png" alt="" /> Back </button>
 +
 +
      <button type="submit" class="next"  onclick="loadnext(3,4);"> Next <img src="images/arrow_right.png" alt=""/> </button>
 +
    </div>
 +
    <ul id="mainNav" class="fiveStep">
 +
      <li class="done"><a href="/" title=""><em>Part 1: Genome Viewer</em></a></li>
 +
      <li class="lastDone"><a href="/" title=""><em>Part 2: Database</em></a></li>
 +
 +
      <li class="current"><a title=""><em>Part 3: Riboswitch Designer</em></a></li>
 +
      <li><a title=""><em>Part 4: Network Illustrator</em></a></li>
 +
      <li class="mainNavNoBg"><a title=""><em>Part 5: Simulator</em> </a></li>
 +
    </ul><div style="clear:both"></div>
 +
  </div>
 +
 +
 +
  <div id="wizardpanel" class="4" >
 +
    <h4>Network Illustrator</h4>
 +
    <div id="wizardcontent" class="softwaretext"><p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Fourthly, to analyze the dynamic change in various metabolic networks, we present a simulator that help the researchers analyze the network in silico, in method of flux balance analysis (FBA).</p> <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Simulator is a tool to analyze target metabolic network in method of flux balance analysis (FBA). The Simulator would help researchers rebuild the metabolic network and search key genes in the network, in order to simplify the synthesis design. Relying on the KEGG Pathway database, a novel rFBA model is formed when regulation-relevant conditions are added into the primitive FBA model, which would help the researchers observe the dynamic change in the metabolic system. Moreover, unlike the mainstream of FBA, the analysis of the Simulator is not based on Matlab and is simple for users.</p></div>
 +
    <div class="buttons">
 +
      <button type="submit" class="previous" onclick="loadnext(4,3);"> <img src="images/arrow_left.png" alt="" /> Back </button>
 +
      <button type="submit" class="next" onclick="loadnext(4,5);"> Next <img src="images/arrow_right.png" alt="" /> </button>
 +
 +
    </div>
 +
    <ul id="mainNav" class="fiveStep">
 +
      <li class="done"><a href="/" title=""><em>Part 1: Genome Viewer</em></a></li>
 +
      <li class="done"><a href="/" title=""><em>Part 2: Database</em></a></li>
 +
      <li class="lastDone"><a href="/" title=""><em>Part 3: Riboswitch Designer</em></a></li>
 +
      <li class="current"><a title=""><em>Part 4: Network Illustrator</em></a></li>
 +
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Revision as of 10:59, 13 July 2012

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> HomeHTML/CSSJavaScriptResourcesT

Project

We have inclination to develop a multifunctional toolbox “Blablabla”, that integrates different modules together and help researchers approach information they need.

SOFTWARE

Genome Viewer

       Firstly, we consider the Genome Viewer, which visualizes the E coli genome, locates the genes on the genome and make it easy to study the characteristics of the genome.

      With this Genome Browser, researchers can approach most information on biotechnology. Users are able to search Biobricks, plasmids and genomes of model microorganisms, in the same time, gene annotations and information of GenBank are presented. The protein sequence is also showed according to the DNA sequences. Aside from searching sequences, users can also input or modify the sequences, insert annotation and build target plasmids they need. The Genome Browser support the format of FASTA when import and export the sequences.

Database

      Secondly, to meet the need of protein-protein interaction researches, we optimize the methods of scanning and output of the existing database, and also supplement the biological information by building novel database.

      This part of the software focus on the design of regulatory elements of metabolic networks, mainly non-coding RNAs including SiRNA and Riboswitch. When a certain gene or protein is given, the Designer would generate the elements. What’s more, the primary and secondary structure can be predicted and presented in the Designer. The function of structure prediction can be also applied in other non-coding RNAs, for instance, microRNAs.

Riboswitch Designer

      Thirdly, we develop a Riboswitch Designer, to help the design of riboswitch, a thriving method applied in biological research, by building an optimized algorithm.

      Relying on the KEGG Pathway database, the Illustrator exports the optimized relevant pathway map of a gene or transcription factor the user interests in.

Network Illustrator

      Fourthly, to analyze the dynamic change in various metabolic networks, we present a simulator that help the researchers analyze the network in silico, in method of flux balance analysis (FBA).

      Simulator is a tool to analyze target metabolic network in method of flux balance analysis (FBA). The Simulator would help researchers rebuild the metabolic network and search key genes in the network, in order to simplify the synthesis design. Relying on the KEGG Pathway database, a novel rFBA model is formed when regulation-relevant conditions are added into the primitive FBA model, which would help the researchers observe the dynamic change in the metabolic system. Moreover, unlike the mainstream of FBA, the analysis of the Simulator is not based on Matlab and is simple for users.

Simulator

      Further, to make it more convenient, the software is localized; that is to say, all functions mentioned above can be achieved without linkage to Internet.

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