Difference between revisions of "Team:Technion Israel/Collaborations"

 
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     <meta charset="utf-8">
 
     <meta charset="utf-8">
 
     <meta name="navbar" content="width=device-width, initial-scale=1">
 
     <meta name="navbar" content="width=device-width, initial-scale=1">
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        <!-- ===================DELETE THIS SECTION WHEN UPLOADING. WE ALREADY HAVE IT IN THE NAVBAR=================== -->
 
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<!-- ===================Basic Bootstrap's CSS and JS=================== -->
 
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            <!-- Bootstrap CSS -->
 
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                <link rel="stylesheet" type="text/css" href="https://2016.igem.org/Team:Technion_Israel/bootstrap.min.css/CSS?action=raw&ctype=text/css"/>
 
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                <link rel="stylesheet" type="text/css" href="https://2016.igem.org/Team:Technion_Israel/bootstrap-theme.min.css/CSS?action=raw&ctype=text/css"/>
 
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            <!-- Bootstrap JS -->
 
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                <script type="text/javascript" src="https://2016.igem.org/Team:Technion_Israel/jquery-2.1.1.min.js/Javascript?action=raw&ctype=text/javascript"></script>
 
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                <script type="text/javascript" src="https://2016.igem.org/Team:Technion_Israel/bootstrap.min.js/Javascript?action=raw&ctype=text/javascript"></script>
 
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            <!-- Our wiki CSS -->
 
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                <link rel="stylesheet" type="text/css" href="https://2016.igem.org/Team:Technion_Israel/CSS?action=raw&ctype=text/css"/>
 
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        <!-- =============================================DELETE UP TO HERE============================================= -->
 
  
  
 
<style>/* inline page CSS */
 
<style>/* inline page CSS */
 
 
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/* ========== general CSS ========== */
 
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/* Body */
 
 
body {
 
body {
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/* font-size: 14px; */  /* optional settings */
 
 
}
 
}
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/* ========== END: general CSS ========== */
 
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/* ==========Background and effects ========== */
 
/* ==========Background and effects ========== */
 
/*Make sure the div is unuiqe to each page*/
 
/*Make sure the div is unuiqe to each page*/
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.collaborations_wrapper {
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.intein_wrapper {
 
position: relative;
 
position: relative;
 
 
 
background: white; /* For browsers that do not support gradients */
 
background: white; /* For browsers that do not support gradients */
−
background: -webkit-linear-gradient(white, #f4f0d0, white); /* For Safari 5.1 to 6.0 */
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background: -webkit-linear-gradient(white, #ecf7fb, white); /* For Safari 5.1 to 6.0 */
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background: -o-linear-gradient(white, #f4f0d0, white); /* For Opera 11.1 to 12.0 */
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background: -o-linear-gradient(white, #ecf7fb, white); /* For Opera 11.1 to 12.0 */
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background: -moz-linear-gradient(white, #f4f0d0, white); /* For Firefox 3.6 to 15 */
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background: -moz-linear-gradient(white, #ecf7fb, white); /* For Firefox 3.6 to 15 */
−
background: linear-gradient(white, #f4f0d0, white); /* Standard syntax */
+
background: linear-gradient(white, #ecf7fb, white); /* Standard syntax */
 
/*background-image:url('addres');
 
/*background-image:url('addres');
 
background-size:cover;
 
background-size:cover;
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/* ========== END: and effects ========== */
 
/* ========== END: and effects ========== */
  
 +
.references {
 +
  font-size: 16px;
 +
outline: 1px solid black;
 +
padding: 20px;
 +
}
  
  
−
/* ========== fonts: ========== */
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/*
 +
Object in external CSS sheet:
  
−
/*corecting wiki css */
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nav-tabs, cont_tabs:
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#HQ_page h1, h2, h3, h4, h5, h6{
+
Open diffrent tabs, we uses imgs.
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font-family: "Century Gothic", "CenturyGothic", "AppleGothic", sans-serif;
+
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}
+
  
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#HQ_page p {
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back-to-top:
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font-family: "Candara", "Calibri", "Segoe", "Segoe UI", "Optima", Arial, sans-serif;
+
go back to top. Apears only when going down the page.
  
−
font-size: 18px;
+
cont_box:
−
font-style: normal;
+
The containers (box) which hold the texts and imgs in the page.
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font-variant: normal;
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font-weight: 400;
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line-height: 27px;
+
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}
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/*setting our wiki's css */
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img_cont:
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h1, h2, h3, h4, h5, h6{
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Every in-content-page img needs to have this class of img.
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font-family: "Century Gothic", "CenturyGothic", "AppleGothic", sans-serif;
+
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color: black;
+
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}
+
  
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p {
+
no-title-col:
−
font-family: "Candara", "Calibri", "Segoe", "Segoe UI", "Optima", Arial, sans-serif;
+
Every in-content-page img needs to have this class of col.
 +
*/
  
−
font-size: 18px;
+
/*canceling wiki bug (inlarge imgs stuck the page)*/
−
font-style: normal;
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.modal-backdrop {
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font-variant: normal;
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position: relative;
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font-weight: 400;
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}
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line-height: 27px;
+
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}
+
  
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/* ========== END: fonts ========== */
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</style>
  
  
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<script>
  
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/* ==========Containers  ========== */
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//up arrow:
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$(document).ready(function(){
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/* Upper section */
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$(window).scroll(function () {
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.collaboration_logo{
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if ($(this).scrollTop() > 350) {
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/*-webkit-filter: grayscale(0.75);*/
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$('#back-to-top').fadeIn();
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cursor: pointer;
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} else {
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transition: all .5s ease;
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$('#back-to-top').fadeOut();
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box-shadow: 5px 5px 3px grey;
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}
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/* border: 2px solid #bbb;
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});
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padding: 15px; */
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// scroll body to 0px on click
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}
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$('#back-to-top').click(function () {
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$('#back-to-top').tooltip('hide');
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$('body,html').animate({
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scrollTop: 0
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}, 800);
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return false;
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});
 +
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$('#back-to-top').tooltip('show');
  
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.collaboration_logo:hover{
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});
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-webkit-filter: grayscale(0);
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////////////////////////
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transform: scale(1.2,1.2);
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//Code: inlarge img on click:
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box-shadow: 5px 5px 3px grey;
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$(function() {
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/*border: 2px solid #000; */
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$('.pop').on('click', function() {
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}
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$('.imagepreview').attr('src', $(this).find('img').attr('src'));
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$('#imagemodal').modal('show');  
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});
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});
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//////////////////////
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///pop-ups:
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$(document).ready(function(){
 +
$('[data-toggle="popover"]').popover();  
 +
});
  
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/* Content section */
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$(function () {
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/* The containers which hold the texts and imgs */
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$('button').popover();
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.coll_par{
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});
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padding-top: 30px;
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padding-right: 30px;
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padding-bottom: 30px;
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padding-left: 30px;
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border-radius:10px;
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/* border-radius:5px;
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background-color: #fff;
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border: 1px solid #000;
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box-shadow: 10px 10px 5px #f4f4f4; */
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}
+
  
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/* ==========END: containers  ========== */
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/* ========== Images CSS  ========== */
 
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.img-peshawar {
 
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margin: auto;
 
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padding: 15px;
 
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border-radius:25px;
 
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}
 
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.no-title-col {
 
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padding-top: 50px;
 
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vertical-align: middle;
 
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}
 
  
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/* ========== End: Images CSS  ========== */
 
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</style>
 
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<script>
 
 
</script>
 
</script>
  
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<!-- ===== One overall container (wrapper) ===== -->
 
<!-- ===== One overall container (wrapper) ===== -->
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<div class="collaborations_wrapper">
+
<div class="intein_wrapper">
  
  
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<div class="row">
 
<div class="row">
 
<div class="col-xs-12">
 
<div class="col-xs-12">
−
<img src="https://static.igem.org/mediawiki/2016/b/b0/T--Technion_Israel--collaboration_cover.jpg" class="img-responsive img-center collaboration_cover" width="100%">
+
<img src="https://static.igem.org/mediawiki/2016/9/9e/T--Technion_Israel--Collaborationcov.jpg" class="img-responsive img-center cont_cover" width="100%">
 
</div>
 
</div>
 
</div>
 
</div>
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<!-- =============== Tabs names: =============== -->
 
<!-- =============== Tabs names: =============== -->
 
<div class="row">
 
<div class="row">
−
<div class="col-md-12">
+
<div class="col-sm-8 col-sm-offset-2"><!-- 8/12 -->
 +
 
 
 
 
<ul class="nav nav-tabs" role="tablist">
 
<ul class="nav nav-tabs" role="tablist">
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<li role="presentation" class="col-sm-3 col-xs-6">
 
<li role="presentation" class="col-sm-3 col-xs-6">
 
<a href="#Peshawar" aria-controls="Peshawar" role="tab" data-toggle="tab">
 
<a href="#Peshawar" aria-controls="Peshawar" role="tab" data-toggle="tab">
−
<img src="https://static.igem.org/mediawiki/2016/b/b2/T--Technion_Israel--peshawar350x250.jpg" class="img-responsive img-center collaboration_logo" width="175" height="125">
+
<img src="https://static.igem.org/mediawiki/2016/1/13/T--Technion_Israel--pashawar.png" class="img-responsive img-center cont_tabs" width="175" height="125">
−
<br><h4 class="text-center"><b>iGEM Peshawar</b></h4>
+
<br><h4 class="text-center"><b>Peshawar</b></h4>
 
</a>
 
</a>
 
</li>
 
</li>
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<li role="presentation" class="col-sm-3 col-xs-6">
 
<li role="presentation" class="col-sm-3 col-xs-6">
 
<a href="#Aachen" aria-controls="Aachen" role="tab" data-toggle="tab">
 
<a href="#Aachen" aria-controls="Aachen" role="tab" data-toggle="tab">
−
<img src="https://static.igem.org/mediawiki/2016/8/8f/T--Technion_Israel--Aachen350x250.jpg" class="img-responsive img-center collaboration_logo" width="175" height="125">
+
<img src="https://static.igem.org/mediawiki/2016/8/8f/T--Technion_Israel--Aachen350x250.jpg" class="img-responsive img-center cont_tabs" width="175" height="125">
−
<br><h4 class="text-center"><b>iGEM Aachen</b></h4>
+
<br><h4 class="text-center"><b>Aachen</b></h4>
 
</a>
 
</a>
 
</li>
 
</li>
  
 
<li role="presentation" class="col-sm-3 col-xs-6">
 
<li role="presentation" class="col-sm-3 col-xs-6">
−
<a href="#BGU" aria-controls="BGU" role="tab" data-toggle="tab">
+
<a href="#Results" aria-controls="Results" role="tab" data-toggle="tab">
−
<img src="https://static.igem.org/mediawiki/2016/2/20/T--Technion_Israel--BGU350x250.jpg" class="img-responsive img-center collaboration_logo" width="175" height="125">
+
<img src="https://static.igem.org/mediawiki/2016/c/c0/T--Technion_Israel--Eindhoven350x250.jpg" class="img-responsive img-center cont_tabs" width="175" height="125">
−
<br><h4 class="text-center"><b>iGEM BGU</b></h4>
+
<br><h4 class="text-center"><b>TU Eindhoven</b></h4>
 
</a>
 
</a>
 
</li>
 
</li>
  
 
<li role="presentation" class="col-sm-3 col-xs-6">
 
<li role="presentation" class="col-sm-3 col-xs-6">
−
<a href="#Eindhoven" aria-controls="Eindhoven" role="tab" data-toggle="tab">
+
<a href="#outlook" aria-controls="outlook" role="tab" data-toggle="tab">
−
<img src="https://static.igem.org/mediawiki/2016/c/c0/T--Technion_Israel--Eindhoven350x250.jpg" class="img-responsive img-center collaboration_logo" width="175" height="125">
+
<img src="https://static.igem.org/mediawiki/2016/2/20/T--Technion_Israel--BGU350x250.jpg" class="img-responsive img-center cont_tabs" width="175" height="125">
−
<br><h4 class="text-center"><b>iGEM Eindhoven</b></h4>
+
<br><h4 class="text-center"><b>BGU</b></h4>
 
</a>
 
</a>
 
</li>
 
</li>
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</div>
 
</div>
 
<!-- ========== End: Tabs panel ========== -->
 
<!-- ========== End: Tabs panel ========== -->
 +
 +
 +
 +
  
  
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<div class="tab-content">
 
<div class="tab-content">
  
−
<!-- =========== Peshawar =========== -->
 
  
−
<div class="row"> <!--Headline-->
+
 
−
<div class="col-sm-12">
+
 
−
<h1 class="text-center"><u>iGEM - Peshawar</u></h1>
+
<!-- =========== 1. Peshawar =========== -->
 +
<div role="tabpanel" class="tab-pane fade in active" id="Peshawar">
 +
<div class="row"> <!--Headline-->
 +
<div class="col-sm-12">
 +
<br>
 +
<h2 class="text-center">Peshawar – Tutoring the first Pakistani team</h2>
 +
</div>
 
</div>
 
</div>
−
</div>
 
  
 +
<!-- ========== Content ========== -->
  
−
<!-- ========== Content ========== -->
+
<div class="row"><!-- #1 row -->
 +
<div class="col-sm-8 col-sm-offset-2"><!-- 8/12 -->
  
 +
<div class="cont_box">
 +
<div class="row">
 +
<div class="col-sm-12">
 +
 +
<div class="col-md-6 col-sm-12">
 +
 +
<p class="text-justify">
 +
<b>We provided guidance to <a href="https://2016.igem.org/Team:Peshawar" ><b>iGEM Peshawar</b></a>, the first team to represent Pakistan. We assisted them with
 +
various aspects of Mathematical Modelling, Human Practice and cloning.</b><br>
 +
<br>
 +
An opportunity for collaboration unveiled itself when we learned that the Pakistani team from Peshawar
 +
University is focusing on detection as a project. During the initial conversation we were amazed to learn
 +
that the said group is the first Pakistani team to compete in iGEM, thus they were in need of guidance with
 +
most aspects of the competition. We decided to aid them and share all the knowledge and experience that
 +
was accumulated in our project and in past Technion iGEM teams. To achieve this, we used different
 +
platforms for communications mainly a Facebook group, where the Peshawar team could get an immediate
 +
answer to any question they had, and multiple Skype sessions each with a different focus such as
 +
mathematical modeling, Human practices, Cloning and more.
 +
</p>
 +
</div>
  
 +
<div class="col-md-6 col-sm-12">
 +
<br><br><br><br>
 +
<a class="pop">
 +
<img src="https://static.igem.org/mediawiki/2016/thumb/8/82/T--Technion_Israel--peshawarSkype1.png/800px-T--Technion_Israel--peshawarSkype1.png" class="img-responsive img-center img-cont" style="cursor: pointer;"><br>
 +
</a>
  
−
<div class="row"><!-- #1 row -->
+
</div>
−
<div class="col-sm-10 col-sm-offset-1">
+
−
<div class="coll_par">
+
−
<div class="row">
+
−
<a id="guidance"></a>
+
−
<div class="col-sm-12">
+
−
+
−
<div class="col-md-6 col-sm-12">
+
−
<h2 class="">Guidance</h2>
+
−
<p class="text-justify">
+
−
At the beginning we contacted Peshawar iGEM group because we discovered that both projects deal with detection.
+
−
When we realized that the Peshawar group is the first team to represent Pakistan in iGEM we decided to share with
+
−
them the knowledge that was accumulated from past Technion iGEM teams.  The first step was to open a joint Facebook
+
−
group, so each team member from every group would be able to find his colleague on the opposite team.
+
−
Later, we had Skype sessions regarding mathematical modeling, Human practices and Cloning.
+
−
</p>
+
−
</div>
+
  
−
<div class="col-md-6 col-sm-12 no-title-col">
+
−
<img src="http://freshdirtdesigns.com/blog/wp-content/uploads/2011/12/image_350x200_placeholder.png" class="img-responsive img-center img-peshawar">
+
</div>
−
</div>
+
  
 +
</div>
 
</div>
 
</div>
 
</div>
 
</div>
 
</div>
 
</div>
−
</div>
 
−
</div><!-- END: #1 row -->
 
  
−
<br>
 
  
−
<div class="row"><!-- #2 row -->
+
<br>
−
<div class="col-sm-10 col-sm-offset-1">
+
−
<div class="coll_par">
+
−
<div class="row">
+
−
<a id="modeling"></a>
+
−
<div class="col-sm-12">
+
  
−
<div class="col-md-6 col-sm-12 new-row no-title-col">
+
<div class="row"><!-- #2 row -->
−
<img src="http://freshdirtdesigns.com/blog/wp-content/uploads/2011/12/image_350x200_placeholder.png" class="img-responsive img-center img-peshawar">
+
<div class="col-sm-8 col-sm-offset-2"><!-- 8/12 -->
−
</div>
+
 
 +
<div class="cont_box">
 +
<div class="row">
 +
<div class="col-sm-12">
 +
 
 +
<div class="col-md-12 col-sm-12">
 +
<h2 class="">Mathematical modeling</h2>
 +
<p class="text-justify">
 +
We aided in the modeling process of Peshawar’s system, specifically using differential equations and logic gates.
 +
The aim of the model was to predict the expression of the reporter protein as a function of the inducers’ concentration (<a href="https://static.igem.org/mediawiki/2016/5/55/T--Technion_Israel--Peshawar_model.pdf" >View PDF</a>).<br>
 +
</p>
 +
 +
</div>
  
−
<div class="col-md-6 col-sm-12">
 
−
<h2 class="">Mathematical modeling</h2>
 
−
<p class="text-justify">
 
−
We modeled Peshawar iGEM group's system using differential equations and logic gates. The aim of the work was
 
−
to predict the expression of the reporter protein when the concentration of the inducer is given.
 
−
<b>צריך לבקש מנופר שתעבור על זה</b>
 
−
</p>
 
 
</div>
 
</div>
 +
</div>
 +
</div>
 +
</div>
 +
</div><!-- END: #2 row -->
  
 +
<br>
 +
 +
 +
<div class="row"><!-- #3 row -->
 +
<div class="col-sm-8 col-sm-offset-2"><!-- 8/12 -->
 +
 +
<div class="cont_box">
 +
<div class="row">
 +
<div class="col-sm-12">
 +
 +
<div class="col-md-6 col-sm-12">
 +
<h2 class="">Cloning</h2>
 +
<p class="text-justify">
 +
The Peshawar team had issues with the plasmid transformations into competent cells. After we got
 +
a full report on the exact steps they followed, we helped debugging their protocol.<br>
 +
We also shared our protocols of chemical transformation and competent cells preparation with them.<br>
 +
These instructions helped the team overcome their obstacles and proceed with the project.
 +
</p>
 +
</div>
 +
 +
 +
<div class="col-md-6 col-sm-12">
 +
<h2 class="">Human practices</h2>
 +
<p class="text-justify">
 +
We shared the layout of our educational program with Peshawar. Moreover, we advised the team regarding
 +
an appeal to the government with a request to promote the education in the field of Synthetic Biology.
 +
</p>
 +
</div>
 +
 +
</div>
 
</div>
 
</div>
 
</div>
 
</div>
 +
</div>
 +
</div><!-- END: #3 row -->
 +
 +
<br>
 +
</div>
 +
<!-- =========== END: Intro =========== -->
 +
 +
 +
 +
<!-- =========== 2: conection to the project =========== -->
 +
<div role="tabpanel" class="tab-pane fade" id="Aachen">
 +
<div class="row"> <!--Headline-->
 +
<div class="col-sm-12">
 +
<br>
 +
<h2 class="text-center">Aachen- Prediction of mutated Subtilisin E protease</h2>
 
</div>
 
</div>
 
</div>
 
</div>
−
</div><!-- END: #2 row -->
 
  
−
<br>
 
  
−
<div class="row"><!-- #3 row -->
+
<!-- ========== Content ========== -->
−
<div class="col-sm-10 col-sm-offset-1">
+
−
<div class="coll_par">
+
−
<div class="row">
+
−
<a id="human"></a>
+
−
<div class="col-sm-12">
+
  
−
<div class="col-md-6 col-sm-12">
 
−
<h2 class="">Human prctices</h2>
 
−
<p class="text-justify">
 
−
We shared with Peshawar iGEM group the layout of our educational program.
 
−
In addition, we gave the team advices regarding an appeal to the government with a
 
−
request to promote the education in the field of Synthetic Biology.
 
−
</p>
 
−
</div>
 
  
−
<div class="col-md-6 col-sm-12 no-title-col">
+
<div class="row"><!-- #1 row -->
−
<img src="http://freshdirtdesigns.com/blog/wp-content/uploads/2011/12/image_350x200_placeholder.png" class="img-responsive img-center img-peshawar">
+
<div class="col-sm-8 col-sm-offset-2"><!-- 8/12 -->
−
</div>
+
 
 +
<div class="cont_box">
 +
<div class="row">
 +
<div class="col-md-12 col-sm-12">
 +
 +
<p class="text-justify">
 +
<b>We met with experts from the Technion to help us visualize the Subtilisin E and the photocaged serine in order to obtain insights regarding the structure of the mutated protein.</b><br>
 +
<br>
 +
We contacted iGEM Aachen when we learned their project deals with protein inactivation, as we believed it might correspond with our Intein sub-project. After discussing the details, we concluded that the Intein protein would not be applicable to Aachen's system. Nevertheless, we decided to collaborate on different aspects of our projects.<br>
 +
<br>
 +
iGEM Aachen asked us to visualize and model the structure of the Subtilisin E protease, which is mutated with a photo caged serine as part of their project.<br>
 +
After consulting with several professors from the faculty of Biology,
 +
we concluded that it would be impossible to finish this task properly in our time period. As an alternative, we wrote a document describing the steps for an exhaustive computational work, including insights from the comparison of the structures of Subtilisin E and the photo-caged serine. (<a href="https://static.igem.org/mediawiki/2016/d/d1/T--Technion_Israel--Aachen_model.pdf" >View PDF</a>).<br>
 +
Finally, we constructed a 3D visualization of Subtilisin E adjacent to the photo-caged serine along with the above document. The information we have obtained was highly valuable and helpful to Aachen’s project.<br>
 +
 
 +
<br>
 +
<br>
 +
 
 +
</p>
 +
</div>
 +
 +
<!-- Mini headline -->
 +
<div class="row">
 +
<div class="col-md-12 col-sm-12">
 +
<h2 class="text-center">Tar fused to GFP marker </h2>
 +
</div>
 +
</div>
 +
 
 +
<!-- 12 text div -->
 +
<div class="row">
 +
<div class="col-md-12 col-sm-12">
 +
<p class="text-justify">
 +
In return, we asked Aachen to build a biobrick consisting of the Tar chemoreceptor fused to a GFP marker.
 +
We provided them all the information necessary for this task (<a href="https://static.igem.org/mediawiki/2016/e/e1/T--Technion_Israel--Aachen_TAR_GFP.pdf" >View PDF</a>).<br>
 +
Aachen's work was successful, providing us with a valuable result on the importance of a linker domain to connect the Tar receptor and the GFP marker. The work made by Aachen had a major significance to our project and we would like to express our gratitude to the Aachen iGEM team for the valuable scientific work they have done for us.<br>
 +
For more information please go to <a href="https://2016.igem.org/Team:Aachen" >Aachen iGEM team’s Wiki page</a>
 +
</p>
 +
</div>
 +
</div>
  
 
</div>
 
</div>
 
</div>
 
</div>
 
</div>
 
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+
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<h2 class="">Cloning</h2>
 
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<p class="text-justify">
 
−
Peshawar had issues with the transformation of plasmids into competent cells.
 
−
They elaborated on the exact steps they did in the lab and we tried to debug their procedure.<br>
 
−
We also shared with team Peshawar our protocol for chemical transformation(3) and the protocol for producing competent cells(4). <br>
 
−
After following our instructions the Peshawar team managed to perform a successful transformation.
 
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</p>
 
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 +
 +
<!-- ==================== 3: TU Eindhoven ==================== -->
 +
<div role="tabpanel" class="tab-pane fade" id="Results">
 +
<div class="row"> <!--Headline-->
 +
<div class="col-sm-8 col-sm-offset-2"><!-- 8/12 -->
 +
 +
<br>
 +
<h2 class="text-center">TU Eindhoven - Writing a manual for the Rosetta software</h2>
 +
</div>
 +
</div>
 +
 +
<!-- ========== Content ========== -->
 +
 +
<div class="row"><!-- #1 row -->
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<div class="col-sm-8 col-sm-offset-2"><!-- 8/12 -->
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 +
<div class="col-sm-12">
 +
 +
<div class="col-md-12 col-sm-12">
 +
<p class="text-justify">
 +
<b>We have written a manual for the operation of the Rosetta software together with <a href="https://2016.igem.org/Team:TU-Eindhoven" ><b>iGEM TU Eindhoven</b></a>.</b><br>
 +
<br>
 +
Our collaboration with iGEM TU Eindhoven was a result of the challenges we faced using the Rosetta software
 +
suite in our project. When we took our very first steps with protein modeling using Rosetta we quickly
 +
discovered numerous problems and difficulties that occupied us for weeks before we even started using the software.<br><br>
 +
During our work, we realized how fast the process could have been if there was a guide detailing the
 +
necessary resources and steps needed for a complete beginner in Rosetta. We figured that this might
 +
be one of the reasons why so few iGEM teams have used Rosetta in the past despite its vast capabilities.<br>
 +
<br>
 +
After getting great results from the software, we decided to share our experience and write this guide
 +
ourselves so that future iGEM teams can have a better starting point. We were delighted to find that
 +
we are not the only team using Rosetta this year and so we contacted iGEM Eindhoven and asked for
 +
their help with the guide. Their work on the guide – writing, sharing their protocols and experience
 +
was a valuable contribution that made the guide much more informative and comprehensive than we initially expected.<a href="https://static.igem.org/mediawiki/2016/5/59/Rosetta_Guide_for_the_iGEM_Beginner.pdf" target="_blank">Click here to see the full guide</a>
 +
<br>
 +
<br>
 +
<br>
 +
</p>
 +
</div>
 +
</div>
 +
<div class="col-md-4 col-md-offset-4 col-sm-12 new-row">
 +
<a class="pop">
 +
<img src="https://static.igem.org/mediawiki/2016/c/ca/T--Technion_Israel--Rosetta_pic.png" class="img-responsive img-center" width="350" height="350" style="cursor: pointer;"><br>
 +
</a>
 +
</div>
 
</div>
 
</div>
 
</div>
 
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 +
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<!-- ==================== 4: BGU ==================== -->
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 +
<div class="row"> <!--Headline-->
 +
<div class="col-sm-8 col-sm-offset-2"><!-- 8/12 -->
 +
 +
<br>
 +
<h2 class="text-center">BGU - Prediction of chemoreceptor-ligand interactions</h2>
 
</div>
 
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+
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 +
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 +
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 +
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 +
<div class="row">
 +
<div class="col-sm-12">
 +
 +
<div class="col-md-12 col-sm-12">
 +
 +
<p class="text-justify">
 +
<b>We processed potential variants of chemoreceptors for <a href="https://2016.igem.org/Team:BGU_ISRAEL" ><b>iGEM BGU</b></a> using the Rosetta software.</b><br>
 +
<br>
 +
We have used the Rosetta software in order to predict protein structure and to check for ligand-protein interactions.
 +
Running the software and processing both the ligand binding domain (LBD) of the Tar chemoreceptor and
 +
BGU's substances of interest - Protocatechuic acid and Ethylene glycol, yielded dozens of LBD variants.<br>
 +
After the filtering process, a library of variants which should theoretically serve as attractant chemoreceptors, was obtained.<br> </p>
 +
</div>
 +
<!-- 12 img div -->
 +
<div class="row">
 +
<div class="col-md-12 col-sm-12">
 +
<a class="pop ocenter">
 +
<img src="https://static.igem.org/mediawiki/2016/7/70/T--Technion_Israel--BGU_visual.png" class="img-responsive img-center img-cont"  style="cursor: pointer;">
 +
</a>
 +
<p class="text-center"><b>Fig. 1:</b> 3D imaging of the variants in the library with the native receptor (wild type), each color represents a different variant. </p>
 +
</div>
 +
</div>
 +
</div>
 +
</div>
 +
</div>
 +
</div>
 +
</div><!-- END: #1 row -->
 +
</div>
 +
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 +
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 +
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 +
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 +
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<a id="back-to-top" href="#" class="btn btn-lg back-to-top" role="button" title="Up" data-toggle="tooltip" data-placement="left"><img src="https://static.igem.org/mediawiki/2016/5/5a/T--Technion_Israel--up_arrow.png" alt=""></a>
  
  

Latest revision as of 01:54, 20 October 2016

S.tar, by iGEM Technion 2016

S.tar, by iGEM Technion 2016


Peshawar – Tutoring the first Pakistani team

We provided guidance to iGEM Peshawar, the first team to represent Pakistan. We assisted them with various aspects of Mathematical Modelling, Human Practice and cloning.

An opportunity for collaboration unveiled itself when we learned that the Pakistani team from Peshawar University is focusing on detection as a project. During the initial conversation we were amazed to learn that the said group is the first Pakistani team to compete in iGEM, thus they were in need of guidance with most aspects of the competition. We decided to aid them and share all the knowledge and experience that was accumulated in our project and in past Technion iGEM teams. To achieve this, we used different platforms for communications mainly a Facebook group, where the Peshawar team could get an immediate answer to any question they had, and multiple Skype sessions each with a different focus such as mathematical modeling, Human practices, Cloning and more.







Mathematical modeling

We aided in the modeling process of Peshawar’s system, specifically using differential equations and logic gates. The aim of the model was to predict the expression of the reporter protein as a function of the inducers’ concentration (View PDF).


Cloning

The Peshawar team had issues with the plasmid transformations into competent cells. After we got a full report on the exact steps they followed, we helped debugging their protocol.
We also shared our protocols of chemical transformation and competent cells preparation with them.
These instructions helped the team overcome their obstacles and proceed with the project.

Human practices

We shared the layout of our educational program with Peshawar. Moreover, we advised the team regarding an appeal to the government with a request to promote the education in the field of Synthetic Biology.



Aachen- Prediction of mutated Subtilisin E protease

We met with experts from the Technion to help us visualize the Subtilisin E and the photocaged serine in order to obtain insights regarding the structure of the mutated protein.

We contacted iGEM Aachen when we learned their project deals with protein inactivation, as we believed it might correspond with our Intein sub-project. After discussing the details, we concluded that the Intein protein would not be applicable to Aachen's system. Nevertheless, we decided to collaborate on different aspects of our projects.

iGEM Aachen asked us to visualize and model the structure of the Subtilisin E protease, which is mutated with a photo caged serine as part of their project.
After consulting with several professors from the faculty of Biology, we concluded that it would be impossible to finish this task properly in our time period. As an alternative, we wrote a document describing the steps for an exhaustive computational work, including insights from the comparison of the structures of Subtilisin E and the photo-caged serine. (View PDF).
Finally, we constructed a 3D visualization of Subtilisin E adjacent to the photo-caged serine along with the above document. The information we have obtained was highly valuable and helpful to Aachen’s project.


Tar fused to GFP marker

In return, we asked Aachen to build a biobrick consisting of the Tar chemoreceptor fused to a GFP marker. We provided them all the information necessary for this task (View PDF).
Aachen's work was successful, providing us with a valuable result on the importance of a linker domain to connect the Tar receptor and the GFP marker. The work made by Aachen had a major significance to our project and we would like to express our gratitude to the Aachen iGEM team for the valuable scientific work they have done for us.
For more information please go to Aachen iGEM team’s Wiki page


TU Eindhoven - Writing a manual for the Rosetta software

We have written a manual for the operation of the Rosetta software together with iGEM TU Eindhoven.

Our collaboration with iGEM TU Eindhoven was a result of the challenges we faced using the Rosetta software suite in our project. When we took our very first steps with protein modeling using Rosetta we quickly discovered numerous problems and difficulties that occupied us for weeks before we even started using the software.

During our work, we realized how fast the process could have been if there was a guide detailing the necessary resources and steps needed for a complete beginner in Rosetta. We figured that this might be one of the reasons why so few iGEM teams have used Rosetta in the past despite its vast capabilities.

After getting great results from the software, we decided to share our experience and write this guide ourselves so that future iGEM teams can have a better starting point. We were delighted to find that we are not the only team using Rosetta this year and so we contacted iGEM Eindhoven and asked for their help with the guide. Their work on the guide – writing, sharing their protocols and experience was a valuable contribution that made the guide much more informative and comprehensive than we initially expected.Click here to see the full guide





BGU - Prediction of chemoreceptor-ligand interactions

We processed potential variants of chemoreceptors for iGEM BGU using the Rosetta software.

We have used the Rosetta software in order to predict protein structure and to check for ligand-protein interactions. Running the software and processing both the ligand binding domain (LBD) of the Tar chemoreceptor and BGU's substances of interest - Protocatechuic acid and Ethylene glycol, yielded dozens of LBD variants.
After the filtering process, a library of variants which should theoretically serve as attractant chemoreceptors, was obtained.

Fig. 1: 3D imaging of the variants in the library with the native receptor (wild type), each color represents a different variant.



< S.tar, by iGEM Technion 2016