Team:Calgary/SandboxMain

From 2012.igem.org

(Difference between revisions)
 
(41 intermediate revisions not shown)
Line 1: Line 1:
 +
{{Team:Calgary/MainHeader}}
 +
<html>
<html>
<!--
<!--
-
Noteable changes:
+
Completed: Epic Box and all rollovers associated with the box.
-
Width of the nav is now increased by 10px. Positions of the dropdowns are also shifted by 10px.
+
Change text in Epic Box to each icon.
-
Firefox gradient for 2-col is fixed.
+
 +
To do: Finish main page
-->
-->
<head>
<head>
Line 15: Line 17:
<style>
<style>
-
 
/*======
/*======
Desktop Styling
Desktop Styling
======*/
======*/
-
 
+
@media only screen and (min-device-width:481px) {
-
/***Nav styling***/
+
-
#nav{
+
/***Body styling***/
-
list-style: none;
+
h1{
-
height: 25em;
+
font-size: 2.5em;
-
width: 190px;
+
-
margin: 0px 10px 0px 10px;
+
-
padding: 20px 0px 20px 10px;
+
-
text-indent: 0;
+
-
float: left;
+
-
+
-
/*Background colours*/
+
-
background: #202020; /*backup colour in case gradients fail*/
+
-
filter: progid:DXImageTransform.Microsoft.gradient(GradientType=1,startColorstr='#202020', endColorstr='#333333'); /* for IE 6+7*/
+
-
-ms-filter:
+
-
"progid:DXImageTransform.Microsoft.gradient(GradientType=1,startColorstr='#202020', endColorstr='#333333')"; /* for IE 8*/
+
-
background: -webkit-gradient(linear, left top, right top, from(#202020), to(#333333)); /* for webkit browsers */
+
-
background: -moz-linear-gradient(left,  #202020,  #333); /* for firefox 3.6+ */
+
-
background: linear-gradient(left, #202020 0%, #333333 100%); /*standard*/
+
-
}
+
-
/*To be moved to JQ block*/
+
-
#menu-icon{
+
-
display: none;
+
-
}
+
-
#nav li{
+
-
height: auto;
+
-
padding: 0;
+
-
}
+
-
/*submenu styling*/
+
-
#nav li a{
+
-
display: block;
+
-
font-family: Myriad Pro, Gill Sans MT, Trebuchet MS, Arial, Sans-Serif;
+
-
color: white;
+
-
font-size: 1.5em;
+
-
line-height: 1.2em; /*line spacing between submenu rows*/
+
-
text-indent: 0.8em;
+
-
letter-spacing: 0.08em;
+
}
}
-
#nav li a.dropheader{
+
h2{
-
text-indent: 0;
+
-
margin-top: 1.3em;
+
-
}
+
-
/*primary menu styling*/
+
-
#nav li > a{
+
-
display: block;
+
-
font-family: Myriad Pro, Gill Sans MT, Trebuchet MS, Arial, Sans-Serif;
+
font-size: 1.8em;
font-size: 1.8em;
-
color: white;
 
-
line-height: 1.4em; /*centers the text vertically*/
 
}
}
-
/*arrows to signify dropout menus; to be moved to JQ block*/
+
 
-
#nav li a.drop:after{
+
#box1{
-
content: '>';
+
width: 968px;
-
padding-right: 20px;
+
margin-top: -8px;
-
color: #BBB;
+
background: #CCCCCC;
-
display: inline;
+
padding-bottom: 20px;
-
float: right;
+
margin-bottom: 13px;
-
}
+
-
#nav li a:hover, #nav li a:hover::after{
+
-
display: block;
+
-
text-decoration: none;
+
-
color: #43bbff;
+
}
}
-
/*mega dropdown styling*/
+
#box1 h2{
-
#nav li div{
+
padding: 20px 20px 20px 20px;
-
position: absolute;
+
-
filter: progid:DXImageTransform.Microsoft.gradient(GradientType=1,startColorstr='#333333', endColorstr='#424242'); /* for IE 6+7*/
+
-
-ms-filter:
+
-
"progid:DXImageTransform.Microsoft.gradient(GradientType=1,startColorstr='#333333', endColorstr='#424242')"; /* for IE 8*/
+
-
background: -webkit-gradient(linear, left top, right top, from(#333333), to(#424242)); /* for webkit browsers */
+
-
background: -moz-linear-gradient(left,  #333333,  #424242); /* for firefox 3.6+ */
+
-
background: linear-gradient(left, #333333 0%, #424242 100%); /*standard*/
+
-
}
+
-
/*1-column styles*/
+
-
#nav li div.col_1{
+
-
left: -999px;
+
-
width: auto;
+
-
padding-bottom: 1.5em;
+
-
}
+
-
#nav li div.col_1 a{
+
-
display: block;
+
-
padding: 0 1.5em;
+
}
}
-
#nav li:hover div.col_1{
+
#box1 p{
-
left: 215px;
+
padding: 0px 20px 0px 20px;
-
margin-top: -55px;
+
font-size: 1.1em;
}
}
-
/*2-column styles*/
+
-
#nav li div.col_2{
+
/***positioning of elements in ZE EPIC BOX***/
-
width: auto;
+
#epicbox{
-
left: -999em;
+
margin-top: 4px;
-
padding-bottom: 1.5em;
+
-
height: auto;
+
-
filter: progid:DXImageTransform.Microsoft.gradient(GradientType=1,startColorstr='#333333', endColorstr='#424242'); /* for IE 6+7*/
+
-
-ms-filter:
+
-
"progid:DXImageTransform.Microsoft.gradient(GradientType=1,startColorstr='#333333', endColorstr='#424242')"; /* for IE 8*/
+
-
background: -webkit-gradient(linear, left top, right top, from(#333333), to(#424242)); /* for webkit browsers */
+
-
background: -moz-linear-gradient(left,  #333333,  #424242); /* for firefox 3.6+ */
+
}
}
-
#nav li div.col_l, #nav li div.col_r{
+
-
position: relative;
+
#boximgcontainer{
-
width: auto;
+
float: left;
float: left;
-
background: transparent;
+
width: 644px;
-
padding-left: 20px;
+
height: 655px;
-
padding-right: 20px;
+
}
}
-
#nav li div.col_l a, #nav li div.col_r a{
+
#boximgcontainer div{
-
display: block;
+
float: left;
 +
position: relative;
 +
}
 +
#orangebox{
 +
margin-bottom: 4px;
 +
}
 +
#orangebox .imgbox{
 +
width: 644px;
 +
height: 215px;
 +
top: 108px;
 +
background: #F6A82D;
 +
margin-bottom: 4px;
}
}
-
#nav li:hover div.col_2{
+
.oblank{
-
left: 215px;
+
width: 644px;
-
margin-top: -55px;
+
height: 104px;
 +
background: #FFE485;
 +
position: relative;
 +
top: -219px;
 +
}
 +
#orangebox:hover .oblank, .oblank:hover{
 +
display: none;
 +
}
 +
#orangebox .iconcontainer{
 +
position: relative;
 +
display: none;
 +
left: auto;
 +
top: -219px;
 +
}
 +
.iconbox div, .iconbox{
 +
width: 104px;
 +
height: 104px;
 +
margin-right: 4px;
 +
}
 +
a.obox1 div{
 +
background: #FFD35A;
 +
}
 +
a.obox2 div{
 +
background: #FECC44;
 +
}
 +
a.obox3 div{
 +
background: #F8C22E;
 +
}
 +
a.obox4 div{
 +
background: #F8B32E;
 +
}
 +
a.obox5 div{
 +
background: #F6A82D;
 +
}
 +
a.obox6 div{
 +
background: #F39808;
 +
margin-right: 0;
 +
}
 +
#orangebox div:hover, #orangebox div.iconbox:hover div{
 +
background: #FFE44F;
 +
}
 +
#orangebox:hover .iconcontainer{
 +
display: block;
 +
background: transparent;
 +
}
 +
 +
 +
#greenbox .imgbox{
 +
width: 320px;
 +
height: 215px;
 +
background: #58CD45;
 +
}
 +
.gblank{
 +
width: 320px;
 +
height: 104px;
 +
background: #A5FF8E;
 +
position: relative;
 +
top: 219px;
 +
left: -320px;
 +
}
 +
#greenbox .iconcontainer{
 +
position: relative;
 +
margin-top: 4px;
 +
left: -999em;
 +
z-index: 1;
 +
}
 +
a.gbox1 div{
 +
background: #72E85B;
 +
}
 +
a.gbox2 div{
 +
background: #5BCD45;
 +
}
 +
a.gbox3 div{
 +
background: #4CC035;
 +
}
 +
a.gbox4 div{
 +
background: #44AF2F;
 +
}
 +
#greenbox div:hover, #greenbox div.iconbox:hover div{
 +
background: #94FF7D;
 +
z-index: 99; /*hovers are not overridden by OSCAR boxes*/
 +
}
 +
#greenbox:hover .gblank, .gblank:hover{
 +
display: none;
 +
}
 +
#greenbox:hover .iconcontainer{
 +
left: auto;
 +
background: transparent;
 +
}
 +
 +
#bluebox{
 +
position: relative;
 +
top: -323px;
 +
left: 320px;
 +
}
 +
#bluebox .imgbox{
 +
width: 320px;
 +
height: 215px;
 +
background: #5BB5E8;
 +
margin-left: 4px;
 +
}
 +
.bblank{
 +
width: 320px;
 +
height: 104px;
 +
background: #C5F0F0;
 +
position: relative;
 +
top: 219px;
 +
left: -320px;
 +
z-index: 0;
 +
}
 +
#bluebox .iconcontainer{
 +
position: relative;
 +
margin-top: 4px;
 +
left: -999em;
 +
z-index: 0;
 +
}
 +
a.bbox1 div{
 +
background: #1574AA;
 +
}
 +
a.bbox2 div{
 +
background: #2580B3;
 +
}
 +
a.bbox3 div{
 +
background: #3285B4;
 +
}
 +
a.bbox4 div{
 +
background: #4292BF;
 +
}
 +
a.bbox5 div{
 +
background: #50A2D0;
 +
}
 +
a.bbox6 div{
 +
background: #5BB5E8;
 +
margin: 0;
 +
}
 +
#bluebox div:hover, #bluebox .iconbox:hover div{
 +
background: #7DD7FF;
 +
z-index: 99; /*hovers are not overridden by FRED boxes*/
 +
}
 +
#bluebox:hover .bblank, .bblank:hover{
 +
display: none;
 +
}
 +
#bluebox:hover .iconcontainer{
 +
left: -320px;
 +
background: transparent;
 +
}
 +
 +
#boxinfo{
 +
float: right;
 +
position: relative;
 +
width: 320px;
 +
left: 3px;
 +
background: #555555;
 +
height: 650px;
 +
margin-bottom: 12px;
}
}
-
 
+
#boxinfo h2{
-
/***End nav styling***/
+
color: white;
-
 
+
padding: 20px 20px 0px;
-
/***Headerimage***/
+
}
-
#headerimage{
+
#boxinfo p{
-
width: 947px;
+
color: white;
-
position: relative;
+
padding: 10px 20px 20px;
-
left: 10px;
+
font-size: 1.2em;
-
margin-bottom: 10px;
+
}
-
margin-top: -20px;
+
/*initial boxinfo appearance settings*/
-
}
+
#boxinfo div.orangebox, #boxinfo div.obox1, #boxinfo div.obox2, #boxinfo div.obox3, #boxinfo div.obox4, #boxinfo div.obox5, #boxinfo div.obox6,
-
#css-full{
+
#boxinfo div.greenbox, #boxinfo div.gbox1, #boxinfo div.gbox2, #boxinfo div.gbox3, #boxinfo div.gbox4,
-
display: none;
+
#boxinfo div.bluebox, #boxinfo div.bbox1, #boxinfo div.bbox2, #boxinfo div.bbox3, #boxinfo div.bbox4, #boxinfo div.bbox5, #boxinfo div.bbox6{
-
}
+
display: none;
-
#css-mobi{
+
}
-
display: block;
+
/*bold colours for FRED and OSCAR*/
-
top: 0px;
+
#boxinfo div.greenbox b{
-
}
+
color: #72E85B;
-
 
+
}
-
/***Logo styling***/
+
#boxinfo div.bluebox b{
-
#logo{
+
color: #5EB7F0;
-
position: relative;
+
}
-
top: -145px;
+
#threeboxes{
-
right: 20px;
+
clear: both;
-
float: right;
+
margin-top: 4px;
-
}
+
position: relative;
-
 
+
width: 968px;
-
#logo img{
+
margin-bottom: 12px;
-
width: 260px;
+
-
}
+
-
+
-
/***Body styling***/
+
-
h1{
+
-
font-size: 2.5em;
+
-
}
+
-
h2{
+
-
font-size: 1.8em;
+
-
}
+
-
 
+
-
/***Content styling***/
+
-
.boxtitle{
+
-
font-size: 2em;
+
-
padding-bottom: 0em;
+
-
padding-top: .3em;
+
-
}
+
-
 
+
-
#nav-wrap{
+
-
float: left;
+
-
height: auto;
+
-
}
+
-
 
+
-
#row1wrap{
+
-
float: left;
+
-
width: 100%;
+
-
margin-top: -60px;
+
-
height: 28em;
+
-
overflow: hidden;
+
-
}
+
-
#box1{
+
-
float: left;
+
-
background-color: #CCC;
+
-
width: 717px;
+
-
margin-top: 0px;
+
-
padding: 10px;
+
-
height: 150%;
+
-
}
+
-
 
+
-
 
+
-
#row2wrap{
+
-
float: left;
+
-
width: 947px;
+
-
margin: 14px 10px;
+
-
}
+
-
/*row2wrap div covers both the #fredbox and #oscarbox*/
+
-
#row2wrap div{
+
-
width: 465px;
+
-
height: 280px;
+
}
}
-
#row2wrap div img{
+
#threeboxes a, #threeboxes a div{
 +
width: 320px;
 +
height: 155px;
float: left;
float: left;
-
padding-top: 30px;
+
margin-bottom: 12px;
-
padding-left: 15px;
+
-
padding-right: 15px;
+
-
padding-bottom: 30px;
+
}
}
-
+
#threeboxes div h2{
-
#row2wrap div h1, #row2wrap div p{
+
padding: 20px 20px 0px;
-
padding-top: 10px;
+
position: relative;
-
padding-right: 15px;
+
top: -155px;
 +
}
 +
#threeboxes div p{
 +
padding: 0px 20px;
 +
position: relative;
 +
top: -155px;
 +
}
 +
#greybox1{
 +
margin-right: 4px;
 +
background: #58CD45;
 +
}
 +
#greybox1:hover{
 +
background: #94FF7D;
 +
}
 +
#greybox2{
 +
margin-right: 4px;
 +
background: #5BB5E8;
 +
}
 +
#greybox2:hover{
 +
background: #7DD7FF;
 +
}
 +
#greybox3{
 +
margin: 0;
 +
background: #F6A82D;
 +
}
 +
#greybox3:hover{
 +
background: #FFE44F;
 +
}
 +
 +
#sponsorsbox{
 +
clear: both;
 +
position: relative;
 +
width: 968px;
 +
margin: 4px 0px;
 +
background: #EEEEEE;
 +
}
 +
#sponsorsbox h2{
 +
padding: 20px 20px 0px 20px;
}
}
-
+
#sponsorsbox p{
-
#row2wrap div h1{
+
padding: 0px 20px;
-
padding-top: 25px;
+
}
}
-
+
#sponsorsbox table{
-
#fredbox{
+
width: 950px;
-
background-color: #59F052;
+
margin-left: auto;
-
float: left;
+
margin-right: auto;
-
text-decoration: none;
+
background: #EEEEEE;
-
}
+
-
+
-
#fredbox:hover{
+
-
background-color: #81FF74;
+
}
}
-
+
#sponsorsbox td{
-
#oscarbox{
+
padding: 15px 0px;
-
background-color: #79BEFF;
+
width: 300px;
-
float: right;
+
-
text-decoration: none;
+
-
}
+
-
+
-
#oscarbox:hover{
+
-
background-color: #91E0FF;
+
}
}
 +
#sponsorsbox img{
 +
display: block;
 +
margin-right: auto;
 +
margin-left: auto;
 +
}
 +
}
 +
</style>
-
/*wrapper for all the small orange boxes*/
+
<script>
-
.smallboxwrap{
+
jQuery(document).ready(function($){
-
width: 947px;
+
 
-
float: left;
+
//eliminate jsnotice
-
margin: 0px 10px;
+
$('#jsnotice').hide();
-
margin-bottom: 10px;
+
 
-
}
+
/* prepend menu icon */
-
.smallboxwrap a{
+
$('#nav-wrap').prepend('<div id="menu-icon">Menu</div>');
-
text-decoration: none;
+
-
float: left;
+
-
}
+
-
.smallboxwrap div, .smallboxwrap a{
+
/* toggle nav */
-
width: 305px;
+
$("#menu-icon").click(function(){
-
height: 165px;
+
$("#nav").slideToggle('fast');
-
background-position: top;
+
$(this).toggleClass("active");
-
}
+
 
 +
});
-
.smallboxwrap div h1, .smallboxwrap div p{
+
/*epic box info functionality*/
-
padding: 10px 15px;
+
//small icons
-
}
+
$('#boximgcontainer .iconbox').hover(
 +
function(){
 +
var className = $(this).attr('class').split(" ");
 +
var box = className[0];
 +
clearinfo();
 +
$('#boxinfo div.' + box).show();
 +
},
 +
function(){
 +
clearinfo();
 +
$('#boxinfo_default').show();
 +
});
 +
//large icons
 +
$('.imgbox').hover(
 +
function(){
 +
var id = $(this).parent().parent().attr('id');
 +
clearinfo();
 +
$('#boxinfo div.' + id).show();
 +
},
 +
function(){
 +
clearinfo();
 +
$('#boxinfo_default').show();
 +
});
-
.smallboxwrap div h1{
+
/*epic box FRED/OSCAR blank box disappearance*/
-
padding-bottom: 0px;
+
$('#bluebox').hover(
-
padding-top: 25px;
+
function(){
-
}
+
$('.gblank').hide();
 +
$('.bblank').hide();
 +
},
 +
function(){
 +
$('.gblank').show();
 +
$('.bblank').show();
 +
});
-
#sboxteam div{
+
$('#greenbox').hover(
-
background: url('https://static.igem.org/mediawiki/2012/1/18/UCalgary2012_MainPageSmallBoxTeam.png');
+
function(){
-
}
+
$('.gblank').hide();
-
#sboxnotebook div{
+
$('.bblank').hide();
-
background: url('https://static.igem.org/mediawiki/2012/a/af/UCalgary2012_MainPageSmallBoxNotebook.png');
+
},
-
}
+
function(){
-
#sboxoutreach div{
+
$('.gblank').show();
-
background: url('https://static.igem.org/mediawiki/2012/d/d5/UCalgary2012_MainPageSmallBoxOutreach.png');
+
$('.bblank').show();
-
}
+
});
-
#sboxdonate div{
+
-
background-color: #FFCC60;
+
-
}
+
-
#sboxdata div{
+
-
background-color: #FFCA48;
+
-
}
+
-
#sboxfollow div{
+
-
background-color: #FFC62A;
+
-
}
+
-
/*spacing the middle box out*/
+
/*Set stylesheet properly*/
-
#sboxnotebook, #sboxdata{
+
/*Current unusable
-
margin: 0px 16px;
+
if($(window).width() > 0){
 +
$("#pagestyle").attr("href", 'https://2012.igem.org/Team:Calgary/static/basicpagedesktop.css?action=raw');
 +
$("#pagestyle").href += (/\?/.test(this.href) ? '&' : '?') + 'ctype=text/css';
}
}
-
/*all orange boxes hover with the same colour or switch sprites*/
+
$('#css-full').click(function(){
-
#sboxdonate:hover div, #sboxdata:hover div, #sboxfollow:hover div{
+
-
background-color: #FFEE82;
+
});
-
}
+
*/
-
#sboxteam:hover div, #sboxnotebook:hover div, #sboxoutreach:hover div{
+
-
background-position: bottom;
+
-
}
+
-
#sponsorbox{
+
});
-
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<h2>Detect and Destroy: Building FRED and OSCAR</h2>
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<p><b>Naphthenic acids (NAs)</b> are a group of recalcitrant carboxylic acid-containing compounds which are byproducts of the bitumen extraction process in the northern Alberta oil sands. These toxic and corrosive compounds are part of the solid and liquid wastes deposited into large holding areas called <b>tailings ponds</b>, which pose a potential environmental and economic concern to Alberta and to other areas. The University of Calgary 2012 iGEM team aims to develop a collection of NA-sensing and degrading organisms for their <b>detection and bioremediation</b>.</p>
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<a id="logo" href="https://2012.igem.org/Team:Calgary"><img src="https://static.igem.org/mediawiki/2012/4/48/UCalgary2012_White_Low-Res_Official_Logo.png"></img></a>
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<p><b>FRED and OSCAR</b> are the two projects we are working on this year. Take a look at the description below to learn more!</p>
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<a class="dropheader" href="#">BIOSENSOR</a>
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<a href="#">Sensing NAs</a>
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<h1 class="boxtitle">Converting Naphthenic Acids to Biofuels</h1>
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<p>Naphthenic acids (NAs) are a group of recalcitrant carboxylic acid-containing compounds which are byproducts of the bitumen extraction process in the northern Alberta oil sands. These toxic and corrosive compounds are part of the solid and liquid wastes deposited into large holding areas called tailings ponds, which pose a potential environmental and economic concern to Alberta and to other areas. The University of Calgary 2012 iGEM team aims to develop a collection of NA-sensing and degrading organisms for their detection and bioremediation.</p>
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<p>Continuing from the <a href="https://2011.igem.org/Team:Calgary">2011 iGEM team’s work</a> on developing a NA biosensor, our team aims to better characterize a biological system for detection and measurement of NAs and other tailings pond compounds using an electrochemical output. New to this year, our major objective is to develop procedures for the conversion of NAs into useful hydrocarbons. As well, our group aims to develop biological and structural solutions to safety problems found in the scale-up process of synthetic biology industrial applications.</p>
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<img src="https://static.igem.org/mediawiki/2012/4/47/UCalgary2012_EpicBoxFRED_-_Blank.png"></img>
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<p>Finally, we hope to develop a proof-of-concept bioreactor system that will be capable of converting these NAs into clean hydrocarbons suitable for industrial use. By providing both an environmental and economic benefit through the remediation of NAs, the 2012 University of Calgary iGEM team hopes to better facilitate biological methodologies for toxin remediation in Alberta, Canada, and beyond.</p>
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<h1>Meet FRED</h1>
 
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<p>FRED is our Functional, Robust Electrochemical Detector. He helps us detect NAs in tailings pond water by using <i>lacZ</i> to electrochemically measure NAs in a sample. FRED can even measure multiple different compounds simultaneously!
 
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Click here to learn more!
 
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<h1>Meet OSCAR</h1>
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<p>OSCAR is our Optimized System for Carboxylic Acid Remediation. He helps us convert NAs in the tailings ponds into hydrocarbons that can be used for more fuel. OSCAR can purify hydrocarbons by removing sulfur and nitrogen groups from the NAs, too!</p>
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<p>Click here to learn more!</p>
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<h2>The Concept</h2>
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<p>Our project consists of three major components: FRED, OSCAR, and the overarching Human Practices considerations surrounding both of their design. Click on the boxes to your left to learn more about what iGEM Calgary has done so far!</p>
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<h1>Our Team</h1>
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<p>Who are we? What do we do? Where is this "Calgary" place, anyway? Click here to read our team profiles!</p>
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<h2>Human Practices</h2>
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<p>Great consideration was put into our Human Practices component this year, as safety was the guiding principle behind the design of FRED and OSCAR. There are many human outreach initiatives that iGEM Calgary has done this year. Roll over the boxes to see each of them!</p>
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<h1>Notebook</h1>
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<p>Click here to find records of our summer's work, as well as attributions. We would also like to thank everybody who helped us along the way.</p>
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<h2>Video Game</h2>
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<p>Play our iGEM Lab Escape video game! Do you have the lab skills necessary to solve the puzzle your professor gave you and escape the lab?</p>
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<h1>Outreach</h1>
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<p>We helped spread the word on synthetic biology and why it's so great. Click here to see our outreach initiatives, and also to play our video game!</p>
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<div class="obox2">
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<h2>Killswitch</h2>
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<p>Both FRED and OSCAR are designed to operate within enclosed environments. However, since safety is our highest priority, we decided to design and implement a killswitch in both FRED and OSCAR as an extra layer of security. The killswitch aims to to destroy the genome using two powerful non-specific nucleases in the unlikely scenario bacteria can escape into the environment. Click here to learn more!</p>
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<h2>Interviews</h2>
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<p>As an undergraduate team, we looked into speaking with experts in various fields, including the oil industry, tailings pond management, biotechnology, law, and politics to gather various opinions on our project. How useful is synthetic biology in a tailings pond environment? What design considerations should we include in our project to improve security? What legal policies must we consider before implementing our project?</p>
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<h2>Design Considerations</h2>
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<p>Since safety is the driving force behind our project, we need to ensure the physical design of our biosensor and bioreactor would be able to contain and manage bacterial cultures without allowing any to escape. We needed to build devices that would ensure the safety of both the user and the outside environment during their use. Click here to learn more!</p>
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<h2>Safety</h2>
 +
<p>Click here for our safety page! Here we detail all the safety procedures, certifications, and approvals we have from our University to allow us to work this summer.</p>
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<div class="obox6">
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<h2>Community Outreach</h2>
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<p>iGEM Calgary partnered with a number of different associations to engage the general public about science and synthetic biology. Click here to see what we've done this summer!</p>
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<h2>FRED</h2>
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<p>FRED is our <b>F</b>unctional, <b>R</b>obust <b>E</b>lectrochemical <b>D</b>etector. FRED is responsible for detecting and measuring NAs and is able to produce an electrochemical signal that can be measured. FRED can be used to measure tailings pond samples within minutes, without having to ship them to an off-site lab for testing. Click on FRED to learn more!</p>
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<h2>Detecting NAs</h2>
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<p>We conducted a transposon search for any regulatory elements that may respond to NAs. Click here to learn more!</p>
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<h2>Electrochemical Reporting</h2>
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<p>As a continuation of our 2011 iGEM project, we have designed a replacement for colourmetric assays. Electrochemical reporting can be used to measure miniscule concentrations regardless of how turbid the sample is. Click here to learn more!</p>
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<h2>Modelling</h2>
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<p>We conducted some modelling on FRED's predicted output.</p>
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<h2>Prototyping</h2>
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<p>We built a prototype biosensor in order to give FRED a home. This biosensor device is capable of performing voltage sweeps that will detect specific compounds. Click here to learn more!</p>
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<h2>OSCAR</h2>
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<p>OSCAR is our <b>O</b>ptimized <b>S</b>ystem for <b>C</b>arboxylic <b>A</b>cid <b>R</b>emediation. OSCAR is responsible for converting NAs into hydrocarbons. OSCAR is also capable of removing nitrogen and sulfur groups from NA rings to purify the hydrocarbons produced even further. Click here to learn more!</p>
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<h2>Decarboxylation</h2>
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<p>In order to convert NAs into hydrocarbons, we need to remove the carboxylic acid groups that make NAs acids. We are using the PetroBrick, from the University of Washington's 2011 iGEM team, to cleave off carboxylic acids to produce hydrocarbons. Click here to learn more!</p>
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<h2>Denitrogenation</h2>
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<p>Nitrogen heteroatoms in the ring structures reduce the efficiency of combustion in the final product. OSCAR is able to remove these nitrogen atoms. Click here to see how!</p>
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<h2>Desulfurization</h2>
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<p>OSCAR can remove sulfur atoms trapped in the rings of NAs. Click here to see how!</p>
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<h2>Catechol Degradation</h2>
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<p>Catechol is a common toxic compound found in tailings ponds. We looked into giving OSCAR the ability to degrade catechol, which would also cleave ring structures of NAs.</p>
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<h2>Bioreactor</h2>
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<p>OSCAR needed a home, so we developed an enclosed bioreactor system where NAs can be converted into hydrocarbons for output. Click here to see how we designed the bioreactor!</p>
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<h2>Flux-Variability Analysis</h2>
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<p>We wanted to optimize OSCAR's output of hydrocarbons, so we computationally modelled which genes should be regulated in order to maximize hydrocarbon output. Click here to see what we found out!</p>
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<h1>Donate!</h1>
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<img src="https://static.igem.org/mediawiki/2012/b/b8/UCalgary2012_ThreeBoxTeam.png"></img>
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<p>We appreciate any support from you to help us complete our project and send our team to the Jamboree. Click here to help us reach our goals!</p>
+
<h2>Team</h2>
 +
<p>Who are we? What did we do? Where is this Calgary place, anyway? Click here to read our team profiles!</p>
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<h1>Data Page</h1>
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<img src="https://static.igem.org/mediawiki/2012/9/92/UCalgary2012_ThreeBoxData.png"></img>
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<p>Click here to take a look at a summary of all our research data so far. Details of each project can be found by clicking on FRED and OSCAR above.</p>
+
<h2>Data Page</h2>
 +
<p>Click here to see a summary of all our data collected so far! Details on FRED and OSCAR can be found above.</p>
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<h1>Follow Us!</h1>
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<img src="https://static.igem.org/mediawiki/2012/1/1b/UCalgary2012_ThreeBoxNotebook.png"></img>
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<p>Keep tabs on what we're up to by following our Facebook page and our Twitter feed!</p>
+
<h2>Notebook</h2>
 +
<p>Here is a record of our summer's work. We also want to thank everybody who helped us along the way!</p>
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<h1>Thanks to Our Sponsors!</h1>
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<h2>Thanks to Our Sponsors!</h2>
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Latest revision as of 21:51, 29 September 2012

Detect and Destroy: Building FRED and OSCAR

Naphthenic acids (NAs) are a group of recalcitrant carboxylic acid-containing compounds which are byproducts of the bitumen extraction process in the northern Alberta oil sands. These toxic and corrosive compounds are part of the solid and liquid wastes deposited into large holding areas called tailings ponds, which pose a potential environmental and economic concern to Alberta and to other areas. The University of Calgary 2012 iGEM team aims to develop a collection of NA-sensing and degrading organisms for their detection and bioremediation.

FRED and OSCAR are the two projects we are working on this year. Take a look at the description below to learn more!

The Concept

Our project consists of three major components: FRED, OSCAR, and the overarching Human Practices considerations surrounding both of their design. Click on the boxes to your left to learn more about what iGEM Calgary has done so far!

Human Practices

Great consideration was put into our Human Practices component this year, as safety was the guiding principle behind the design of FRED and OSCAR. There are many human outreach initiatives that iGEM Calgary has done this year. Roll over the boxes to see each of them!

Video Game

Play our iGEM Lab Escape video game! Do you have the lab skills necessary to solve the puzzle your professor gave you and escape the lab?

Killswitch

Both FRED and OSCAR are designed to operate within enclosed environments. However, since safety is our highest priority, we decided to design and implement a killswitch in both FRED and OSCAR as an extra layer of security. The killswitch aims to to destroy the genome using two powerful non-specific nucleases in the unlikely scenario bacteria can escape into the environment. Click here to learn more!

Interviews

As an undergraduate team, we looked into speaking with experts in various fields, including the oil industry, tailings pond management, biotechnology, law, and politics to gather various opinions on our project. How useful is synthetic biology in a tailings pond environment? What design considerations should we include in our project to improve security? What legal policies must we consider before implementing our project?

Design Considerations

Since safety is the driving force behind our project, we need to ensure the physical design of our biosensor and bioreactor would be able to contain and manage bacterial cultures without allowing any to escape. We needed to build devices that would ensure the safety of both the user and the outside environment during their use. Click here to learn more!

Safety

Click here for our safety page! Here we detail all the safety procedures, certifications, and approvals we have from our University to allow us to work this summer.

Community Outreach

iGEM Calgary partnered with a number of different associations to engage the general public about science and synthetic biology. Click here to see what we've done this summer!

FRED

FRED is our Functional, Robust Electrochemical Detector. FRED is responsible for detecting and measuring NAs and is able to produce an electrochemical signal that can be measured. FRED can be used to measure tailings pond samples within minutes, without having to ship them to an off-site lab for testing. Click on FRED to learn more!

Detecting NAs

We conducted a transposon search for any regulatory elements that may respond to NAs. Click here to learn more!

Electrochemical Reporting

As a continuation of our 2011 iGEM project, we have designed a replacement for colourmetric assays. Electrochemical reporting can be used to measure miniscule concentrations regardless of how turbid the sample is. Click here to learn more!

Modelling

We conducted some modelling on FRED's predicted output.

Prototyping

We built a prototype biosensor in order to give FRED a home. This biosensor device is capable of performing voltage sweeps that will detect specific compounds. Click here to learn more!

OSCAR

OSCAR is our Optimized System for Carboxylic Acid Remediation. OSCAR is responsible for converting NAs into hydrocarbons. OSCAR is also capable of removing nitrogen and sulfur groups from NA rings to purify the hydrocarbons produced even further. Click here to learn more!

Decarboxylation

In order to convert NAs into hydrocarbons, we need to remove the carboxylic acid groups that make NAs acids. We are using the PetroBrick, from the University of Washington's 2011 iGEM team, to cleave off carboxylic acids to produce hydrocarbons. Click here to learn more!

Denitrogenation

Nitrogen heteroatoms in the ring structures reduce the efficiency of combustion in the final product. OSCAR is able to remove these nitrogen atoms. Click here to see how!

Desulfurization

OSCAR can remove sulfur atoms trapped in the rings of NAs. Click here to see how!

Catechol Degradation

Catechol is a common toxic compound found in tailings ponds. We looked into giving OSCAR the ability to degrade catechol, which would also cleave ring structures of NAs.

Bioreactor

OSCAR needed a home, so we developed an enclosed bioreactor system where NAs can be converted into hydrocarbons for output. Click here to see how we designed the bioreactor!

Flux-Variability Analysis

We wanted to optimize OSCAR's output of hydrocarbons, so we computationally modelled which genes should be regulated in order to maximize hydrocarbon output. Click here to see what we found out!

Thanks to Our Sponsors!

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