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Team:KULeuven/Project/Filter
From 2008.igem.org
Result:
To have a dropdown for your own team copy over all of the content below. It might be needed to adjust a thing or two. Comments have been added throughout the code what must be changed.
Inspirational websites:
- Most basic dropdown menu, with no submenu's
- The javascript library used to add effects and optimise the dropdown
- How to center a ul list effectively
The dropdown has been created and developed by the KULeuven team.
<html>
<style type="text/css">
#content {z-index:4;}
#ddwrapper * {z-index:8 !important;}
div#ddwrapper {
margin:0;
padding:0;
height:28px;
width:945px; /* change to adjust imperfections in width */
}
div#ddnav {
margin:0 auto; /* needed to center the dropdown */
padding:0;
top:5px;
/* width: 965px */
visibility:hidden; /* dropdown is hidden until properly initalised by javascript */
}
div#ddtoggle {
margin:0;
position:fixed;
right:2px;
top:15px;
height:10px;
width:10px;
z-index:100;
}
#ddnav ul {
display:table-row; /* works only for firefox, later adjusted by javascript for IE */
margin:0 auto;
padding:0;
}
#ddnav ul li {
display:table-cell; /* works only for firefox, later adjusted by javascript for IE */
list-style:none;
margin:0;
padding:0 !important;
border-right:1px solid #FFF; /* creates illusion of spacing between tabs */
}
#ddnav ul li:last-child{border-right:none;}
#ddnav a{
display:block;
margin:0;
padding:4px 14px; /* play with dimensions for size of tabs */
background-color:#075A90; /* background color for tabs */
color:#FFF !important; /* font color for text in tabs */
text-align:center; /* aligning for text in tabs */
text-decoration:none !important;
font:bold 10pt Trebuchet MS; /* font properties for text in tabs */
outline:0;
}
#ddnav ul li a:hover {background-color:#99CCFF;}/* background color for tabs on mouseover */
#ddnav li a:active {outline:none;} /* remove standard dotted border for links when clicked (IE) */
#ddnav li a:focus {-moz-outline-style:none;} /* remove standard dotted border for links when clicked (FF) */
#ddnav div {
display:none;
position:absolute;
width:9em;
background-color:#000; /* bug solution, do not change ! */
border:1px solid #5970B2; /* border color for dropdown menus */
opacity:0.9; /* transparancy of the dropdown menus (FF) */
filter:alpha(opacity=90); /* transparancy of the dropdown menus (IE) */
}
#ddnav div a {
display:block;
padding:5px 10px; /* play with dimensions of block element in dropdown menus */
position:relative;
font:normal 8pt arial; /* font properties for text in dropdown menus */
text-align:left; /* aligning of text in dropdown menus */
cursor:pointer;
}
#ddnav div a:hover, #ddnav span a:hover {color:#000 !important;} /* text color on mouseover */
#ddnav span div {
position:relative;
border:none;
border-bottom:2px groove #5970B2; /* separator for submenus, groove does not work in FF */
opacity:1.0; /* avoid stacking transparancy for submenus (FF) */
filter:alpha(opacity=100); /* avoid stacking transparancy for submenus (IE) */
}
/* may want to upload the following pictures to a new location */
.expand {background: url('https://static.igem.org/mediawiki/2008/e/ef/Icon-expand.png') no-repeat 95% 50%;}
.collapse {background: url('https://static.igem.org/mediawiki/2008/c/cd/Icon-collapse.png') no-repeat 95% 50%;}
.docked {background: #99ccff url("https://static.igem.org/mediawiki/2008/6/62/Ddnavundock.png") no-repeat 50% 50%;}
.undocked {background: #99ccff url("https://static.igem.org/mediawiki/2008/e/e4/Ddnavdock.png") no-repeat 50% 50%;}
</style>
<!-- IMPORTANT: save following script under a personalized webspace or download the library at www.jquery.com -->
<script type="text/javascript" src="http://student.kuleuven.be/~s0173901/wiki/js/jquery.js"></script>
<script type="text/javascript">
function ddnav() {
$('#ddnav ul li').hover(
function () {
$(this).find('div:first').css('display','block');},
function () {
$(this).find('div:first').css('display','none');}
);
}
function ddnavsub() {
$('#ddnav span > a').toggle(
function () {
$(this).removeClass("#ddnav expand").addClass("#ddnav collapse");
$(this).parent().find('div:first').slideDown('fast');
$(this).hover(
function (){$(this).css('background-color','#99AAFF');},
function (){$(this).css('background-color','#99AAFF');});},
function () {
$(this).removeClass("#ddnav collapse").addClass("#ddnav expand");
$(this).parent().find('div:first').css('display','none');
$(this).hover(
function (){$(this).css('background-color','#99CCFF');},
function (){$(this).css('background-color','#075A90');});}
).addClass("#ddnav expand");
}
/* If you wish to omit the docking feature, remove following function ddtoggle() */
function ddtoggle() {
$('#ddtoggle').toggle(
function () {
$(this).removeClass('undocked').addClass('docked');
$('#ddnav').css('position','fixed');},
function () {
$(this).removeClass('docked').addClass('undocked');
$('#ddnav').css('position','static');}
);
}
function ddalign() {
var _windowWidth = $(window).width();
var _leftOffset = (_windowWidth - 965)/2;
$('div#ddnav').css('left',_leftOffset);
}
function ddmsie() {
$('#ddnav a').hover(
function () {$(this).css('background-color','#99ccff');},
function () {$(this).css('background-color','#075a90');}
);
/* toggle doesn't work yet */
$('#ddtoggle').css('display','none');
$('#ddnav ul').css('display','inline-block');
$('#ddnav ul li').css('display','inline');
$('#ddnav ul li').css('position','relative');
$('#ddnav ul li>a').css('display','inline-block');
$('#ddnav ul li>a').css('margin-right','-4px');
$('#ddnav div').css('left','0');
$('#ddnav div').css('top','100%');
$('#ddnav span div').css('top','0');
}
function ddmozilla() {
ddtoggle();
$(window).bind('resize', function() {ddalign();});
}
$(function () {
ddnav();
ddnavsub();
if(jQuery.browser.msie) ddmsie();
if(jQuery.browser.mozilla) ddmozilla();
$('#ddnav').css('visibility','visible');
});
</script>
<!-- If you wish to omit the docking feature omit following line (div with id ddtoggle) -->
<div id="ddtoggle" class="undocked"></div>
<div id="ddwrapper">
<!-- Here the actual links are defined, simply replace with your own links in the appropriate sections -->
<div id="ddnav" align="center">
<ul>
<li>
<a href="https://2008.igem.org/Team:KULeuven">Home</a>
</li>
<li>
<a>The Team</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Team/LabsandGroups">Research Labs and Groups</a>
<a href="https://2008.igem.org/Team:KULeuven/Team/Students">Students</a>
<a href="https://2008.igem.org/Team:KULeuven/Team/Instructors">Instructors</a>
<a href="https://2008.igem.org/Team:KULeuven/Team/Advisors">Advisors</a>
<a href="https://2008.igem.org/Team:KULeuven/Team/Pictures">Pictures</a>
</div>
</li>
<li>
<a>The Project</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Project">Summary</a>
<span>
<a>Components</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Project/Input">Input</a>
<a href="https://2008.igem.org/Team:KULeuven/Project/Output">Output</a>
<a href="https://2008.igem.org/Team:KULeuven/Project/Filter">Filter</a>
<a href="https://2008.igem.org/Team:KULeuven/Project/Inverter">Invertimer</a>
<a href="https://2008.igem.org/Team:KULeuven/Project/Reset">Reset</a>
<a href="https://2008.igem.org/Team:KULeuven/Project/CellDeath">Cell Death</a>
<a href="https://2008.igem.org/Team:KULeuven/Project/Memory">Memory</a>
</div>
</span>
<a href="https://2008.igem.org/Team:KULeuven/Evaluation">End Evaluation</a>
<a href="https://2008.igem.org/Team:KULeuven/Literature">Literature</a>
<a href="https://2008.igem.org/Team:KULeuven/Brainstorm">Brainstorm</a>
</div>
</li>
<li>
<a>Ethics</a>
<div>
</div>
</li>
<li>
<a>Submitted Parts</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Parts">Listing</a>
<a href="http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2008&group=KULeuven">Sandbox</a>
</div>
</li>
<li>
<a>Modeling</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Model/Overview">Overview</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/KineticConstants">Kinetic Constants</a>
<span>
<a>Components</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Model/Output">Output</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/Filter">Filter</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/Inverter">Invertimer</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/Reset">Reset</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/CellDeath">Cell Death</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/Memory">Memory</a>
</div>
</span>
<a href="https://2008.igem.org/Team:KULeuven/Model/FullModel">Full Model</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/Sensitivity">Sensitivity Analysis</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/MultiCell">Multi-cell Model</a>
<a href="https://2008.igem.org/Team:KULeuven/Model/Diffusion">Diffusion</a>
</div>
</li>
<li>
<a>Data Analysis</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Data/Overview">Overview</a>
<span>
<a>New Parts</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Data/GFP">GFP (LVA-tag)</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/T7">T7 (UmuD-tag)</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/Antisense">Antisense LuxI</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/ccdB">Celldeath (ccdB)</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/HybridProm">Hybrid Promotor</a>
</div>
</span>
<span>
<a>Components</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Data/Input">Input</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/Output">Output</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/Filter">Filter</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/Inverter">Invertimer</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/Reset">Reset</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/CellDeath">Cell Death</a>
<a href="https://2008.igem.org/Team:KULeuven/Data/Memory">Memory</a>
</div>
</span>
<a href="https://2008.igem.org/Team:KULeuven/Data/FullModel">Full Model</a>
</div>
</li>
<li>
<a>Software</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Software/MultiCell">Multi-cell Toolbox</a>
<a href="https://2008.igem.org/Team:KULeuven/Software/Simbiology2LaTeX">Simbiology2LaTeX Toolbox</a>
</div>
</li>
<li>
<a>Notebook</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Meeting_Calendar">Calendar</a>
<a href="https://2008.igem.org/Team:KULeuven/SummerHolidays">Summer Holidays</a>
<span>
<a>Reports</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Meeting Reports">Daily</a>
<a href="https://2008.igem.org/Team:KULeuven/Weekly Meetings">Weekly</a>
</div>
</span>
<span>
<a>Lab Data</a>
<div>
<a href="https://2008.igem.org/Team:KULeuven/Freezer">Freezer</a>
<a href="https://2008.igem.org/Team:KULeuven/Primers">Primers</a>
<a href="https://2008.igem.org/Team:KULeuven/Ligation">Ligation</a>
</div>
</span>
<a href="https://2008.igem.org/Team:KULeuven/Tools">Tools</a>
<a href="https://2008.igem.org/Team:KULeuven/Press">Press</a>
<a href="https://2008.igem.org/Team:KULeuven/Guestbook">Guestbook</a>
</div>
</li>
</ul>
</div>
</div>
</html>
Filter
The filter mechanism makes use of a coherent feedforward loop with and gate (reference). For this system, we thus needed a primary messenger, which gives a signal that leads to a secondary messenger, and that is fast degrading. The secondary messenger is a signal that is more stable in time. They cooperate together in the AND-gate to result in another signal. This last signal is the output of the filter.
Among the fast degrading molecules in a bacterial cell are mRNA's. We used the key-lock system as a primary messenger. Upon input signal, BBa_J23009 is transcribed and RiboKey3d is produced. This mRNA has a relatively short lifetime (referentie naar parameters van de ir's). This key can unlock the RiboLock3d, which is part BBa_J23032.
Under the constitutive promoter BBa_I23110, and locked by RiboLock3d, we find BBa_K145xxx, a T7 RNA polymerase with UmuD-derived tag. This T7 RNA polymerase is a protein, and thus much more stable than mRNA. So stable, that modeling proved it was too stable. So a tag has been added to make it degrade faster. A C-terminal LVA tag would probably not have worked, as the C-terminal of T7 RNA polymerase is part of the catalytic region (figuur). An N-terminal tag, however, is the solution to this problem. More information on this N-terminal, UmuD derived tag can be found here (link).
We see now, that production of the RiboLock3d will give rise to T7 RNA polymerase production, and that the requirements concerning the lifetime of the messenger molecules are fulfilled. The T7 promoter and RiboLock3d together now form the AND-gate, giving transcription only when both the T7 RNA polymerase and RiboLock3d are present together.
For more information on the exact kinetics and dynamics of this system, see the modeling page (link).
