Team:ETH Zurich/modeling/overview

From 2014.igem.org

(Difference between revisions)
m
 
(83 intermediate revisions not shown)
Line 1: Line 1:
{{:Team:ETH Zurich/tpl/head|Modeling overview}}
{{:Team:ETH Zurich/tpl/head|Modeling overview}}
-
<html><article>
+
<html>
-
<div style="position:relative; left:0px; top:0px; width:100%;">
+
<script type="text/javascript">
-
<div style="background-image:url(https://static.igem.org/mediawiki/2014/f/f0/ETH_Zurich_Modeling-overview_01.gif); position:absolute; left:0px; top:0px; width:1100px; height:77px;" title="">
+
(function($) {
-
</div>
+
function img(url) {
-
<div style="background-image:url(https://static.igem.org/mediawiki/2014/4/44/ETH_Zurich_Modeling-overview_02.gif); position:absolute; left:0px; top:77px; width:113px; height:1575px;" title="">
+
var i = new Image;
-
</div>
+
i.src = url;
-
<a href="https://2014.igem.org/Team:ETH_Zurich/modeling/qs" style="cursor:hand">
+
return i;
-
<div style="background-image:url(https://static.igem.org/mediawiki/2014/8/8c/ETH_Zurich_Lux-quorum-sensing-module.gif); position:absolute; left:113px; top:77px; width:357px; height:446px;" title="">
+
}
-
</div></a>
+
-
<div style="background-image:url(https://static.igem.org/mediawiki/2014/0/01/ETH_Zurich_Modeling-overview_04.gif); position:absolute; left:470px; top:77px; width:174px; height:1081px;" title="">
+
if ('naturalWidth' in (new Image)) {
-
</div>
+
$.fn.naturalWidth = function() { return this[0].naturalWidth; };
-
<a href="https://2014.igem.org/Team:ETH_Zurich/modeling/qs" style="cursor:hand">
+
$.fn.naturalHeight = function() { return this[0].naturalHeight; };
-
<div style="background-image:url(https://static.igem.org/mediawiki/2014/a/a3/ETH_Zurich_Las-quorum-sensing-module.gif); position:absolute; left:644px; top:77px; width:357px; height:446px;" title="">
+
return;
-
</div></a>
+
}
-
<div style="background-image:url(https://static.igem.org/mediawiki/2014/1/10/ETH_Zurich_Modeling-overview_06.gif); position:absolute; left:1001px; top:77px; width:99px; height:1575px;" title="">
+
$.fn.naturalWidth = function() { return img(this[0].src).width; };
-
</div>
+
$.fn.naturalHeight = function() { return img(this[0].src).height; };
-
<div style="background-image:url(https://static.igem.org/mediawiki/2014/c/cb/ETH_Zurich_Modeling-overview_07.gif); position:absolute; left:113px; top:523px; width:357px; height:85px;" title="">
+
})(jQuery);
-
</div>
+
-
<div style="background-image:url(https://static.igem.org/mediawiki/2014/d/dd/ETH_Zurich_Modeling-overview_08.gif); position:absolute; left:644px; top:523px; width:357px; height:85px;" title="">
+
-
</div>
+
-
<a href="https://2014.igem.org/Team:ETH_Zurich/modeling/int" style="cursor:hand">
+
-
<div style="background-image:url(https://static.igem.org/mediawiki/2014/e/ea/ETH_Zurich_Bxb1-integrase-module.gif); position:absolute; left:113px; top:608px; width:357px; height:446px;" title="">
+
-
</div></a>
+
-
<a href="https://2014.igem.org/Team:ETH_Zurich/modeling/int" style="cursor:hand">
+
-
<div style="background-image:url(https://static.igem.org/mediawiki/2014/a/a4/ETH_Zurich_fC31-integrase-module.gif); position:absolute; left:644px; top:608px; width:357px; height:446px;" title="">
+
-
</div></a>
+
-
<div style="background-image:url(https://static.igem.org/mediawiki/2014/5/5a/ETH_Zurich_Modeling-overview_11.gif); position:absolute; left:113px; top:1054px; width:357px; height:104px;" title="">
+
-
</div>
+
-
<div style="background-image:url(https://static.igem.org/mediawiki/2014/d/d1/ETH_Zurich_Modeling-overview_12.gif); position:absolute; left:644px; top:1054px; width:357px; height:104px;" title="">
+
-
</div>
+
-
<div style="background-image:url(https://static.igem.org/mediawiki/2014/a/a4/ETH_Zurich_Modeling-overview_13.gif); position:absolute; left:113px; top:1158px; width:222px; height:494px;" title="">
+
-
</div>
+
-
<a href="https://2014.igem.org/Team:ETH_Zurich/modeling/overview#xor" style="cursor:hand">
+
-
<div style="background-image:url(https://static.igem.org/mediawiki/2014/2/25/ETH_Zurich_XOR-gate-module.gif); position:absolute; left:335px; top:1158px; width:444px; height:419px;" title="">
+
-
</div></a>
+
-
<div style="background-image:url(https://static.igem.org/mediawiki/2014/0/01/ETH_Zurich_Modeling-overview_15.gif); position:absolute; left:779px; top:1158px; width:222px; height:494px;" title="">
+
-
</div>
+
-
<div style="background-image:url(https://static.igem.org/mediawiki/2014/f/fd/ETH_Zurich_Modeling-overview_16.gif); position:absolute; left:335px; top:1577px; width:444px; height:75px;" title="">
+
-
</div>
+
-
</div>
+
-
<!--
 
-
<?xml version="1.0" encoding="utf-8"?>
 
-
<!-- Generator: Adobe Illustrator 18.0.0, SVG Export Plug-In . SVG Version: 6.00 Build 0)  -->
 
-
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
 
-
<svg  version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px" width="100%"
 
-
viewBox="293.5 -33 374.5 684.7" enable-background="new 293.5 -33 374.5 684.7" xml:space="preserve">
 
-
<rect x="296.8" y="0.2" fill="#FFFFFF" stroke="#000000" stroke-miterlimit="10" width="146.6" height="183.2"/>
 
-
<rect x="516.6" y="0.2" fill="#FFFFFF" stroke="#000000" stroke-miterlimit="10" width="146.6" height="183.2"/>
 
-
<rect x="296.8" y="220.1" fill="#FFFFFF" stroke="#000000" stroke-miterlimit="10" width="146.6" height="183.2"/>
 
-
<rect x="516.6" y="220.1" fill="#FFFFFF" stroke="#000000" stroke-miterlimit="10" width="146.6" height="183.2"/>
 
-
<rect x="389.5" y="448.5" fill="#FFFFFF" stroke="#000000" stroke-width="1.1315" stroke-miterlimit="10" width="181" height="171"/>
 
-
<text transform="matrix(1 0 0 1 312.3166 15.2648)" font-family="'ArialMT'" font-size="9.1623">Lux quorum sensing module</text>
 
-
<text transform="matrix(1 0 0 1 532.2112 15.2641)" font-family="'ArialMT'" font-size="9.1623">Las quorum sensing module</text>
 
-
<text transform="matrix(1 0 0 1 322.65 235.1661)" font-family="'ArialMT'" font-size="9.1623">Bxb1 integrase module</text>
 
-
<text transform="matrix(1 0 0 1 547.2112 235.1662)" font-family="'ArialMT'" font-size="9.1623">φC31 integrase module</text>
 
-
<text transform="matrix(1 0 0 1 447.264 464.2239)" font-family="'ArialMT'" font-size="9.1623">XOR gate module</text>
 
-
<image overflow="visible" width="680" height="287" xlink:href="../Documents/travail/Master ETH/Cours/iGEM/Wiki/reactionsxor.PNG"  transform="matrix(0.2623 0 0 0.2623 390.808 471.0391)">
 
-
</image>
 
-
<image overflow="visible" width="547" height="233" xlink:href="../Documents/travail/Master ETH/Cours/iGEM/Wiki/reactionslas.PNG"  transform="matrix(0.2048 0 0 0.2048 537.3335 22.492)">
 
-
</image>
 
-
<image overflow="visible" width="550" height="240" xlink:href="../Documents/travail/Master ETH/Cours/iGEM/Wiki/reactionslux.PNG"  transform="matrix(0.2169 0 0 0.2169 310.0248 22.492)">
 
-
</image>
 
-
<image overflow="visible" width="403" height="105" xlink:href="../Documents/travail/Master ETH/Cours/iGEM/Wiki/reactionsphic31.PNG"  transform="matrix(0.2095 0 0 0.2095 549.5413 244.5021)">
 
-
</image>
 
-
<image overflow="visible" width="419" height="95" xlink:href="../Documents/travail/Master ETH/Cours/iGEM/Wiki/reactionsbxb1.PNG"  transform="matrix(0.2316 0 0 0.2316 321.1509 244.5021)">
 
-
</image>
 
-
<g>
 
-
<defs>
 
-
<rect id="SVGID_1_" x="300" y="78" width="139.3" height="101.7"/>
 
-
</defs>
 
-
<clipPath id="SVGID_2_">
 
-
<use xlink:href="#SVGID_1_"  overflow="visible"/>
 
-
</clipPath>
 
-
<g clip-path="url(#SVGID_2_)">
 
-
<defs>
 
-
<rect id="SVGID_3_" x="293.5" y="74.6" width="159" height="106.2"/>
 
-
</defs>
 
-
<clipPath id="SVGID_4_">
 
-
<use xlink:href="#SVGID_3_"  overflow="visible"/>
 
-
</clipPath>
 
-
<g clip-path="url(#SVGID_4_)">
 
-
 
-
<image overflow="visible" width="768" height="513" xlink:href="../AppData/Local/Temp/LuxQSModel.jpg"  transform="matrix(0.207 0 0 0.207 293.5458 74.5797)">
 
-
</image>
 
-
</g>
 
-
</g>
 
-
</g>
 
-
<g>
 
-
<defs>
 
-
<rect id="SVGID_5_" x="523.3" y="73.6" width="133" height="108.7"/>
 
-
</defs>
 
-
<clipPath id="SVGID_6_">
 
-
<use xlink:href="#SVGID_5_"  overflow="visible"/>
 
-
</clipPath>
 
-
<g clip-path="url(#SVGID_6_)">
 
-
 
-
<image overflow="visible" width="560" height="419" xlink:href="../AppData/Local/Temp/LasQSModel.jpg"  transform="matrix(0.2643 0 0 0.2643 520.0458 72.3154)">
 
-
</image>
 
-
</g>
 
-
</g>
 
-
<g>
 
-
<g>
 
-
<line fill="none" stroke="#000000" stroke-width="1.1315" stroke-miterlimit="10" x1="370.1" y1="-33" x2="370.1" y2="-5.3"/>
 
-
<g>
 
-
<polygon points="370.1,-1.3 367.8,-7 370.1,-5.6 372.4,-7 "/>
 
-
</g>
 
-
</g>
 
-
</g>
 
-
<g>
 
-
<g>
 
-
<line fill="none" stroke="#000000" stroke-width="1.1315" stroke-miterlimit="10" x1="589.9" y1="-33" x2="589.9" y2="-5.3"/>
 
-
<g>
 
-
<polygon points="589.9,-1.3 587.6,-7 589.9,-5.6 592.2,-7 "/>
 
-
</g>
 
-
</g>
 
-
</g>
 
-
<g>
 
-
<g>
 
-
<line fill="none" stroke="#000000" stroke-width="1.1315" stroke-miterlimit="10" x1="428.3" y1="409.7" x2="428.3" y2="437.3"/>
 
-
<g>
 
-
<polygon points="428.3,441.3 426,435.7 428.3,437 430.6,435.7 "/>
 
-
</g>
 
-
</g>
 
-
</g>
 
-
<g>
 
-
<g>
 
-
<line fill="none" stroke="#000000" stroke-width="1.1315" stroke-miterlimit="10" x1="532.2" y1="409.7" x2="532.2" y2="437.3"/>
 
-
<g>
 
-
<polygon points="532.2,441.3 529.9,435.7 532.2,437 534.5,435.7 "/>
 
-
</g>
 
-
</g>
 
-
</g>
 
-
<g>
 
-
<g>
 
-
<line fill="none" stroke="#000000" stroke-width="1.1315" stroke-miterlimit="10" x1="589.8" y1="186.7" x2="589.8" y2="214.3"/>
 
-
<g>
 
-
<polygon points="589.8,218.3 587.5,212.7 589.8,214 592.1,212.7 "/>
 
-
</g>
 
-
</g>
 
-
</g>
 
-
<g>
 
-
<g>
 
-
<line fill="none" stroke="#000000" stroke-width="1.1315" stroke-miterlimit="10" x1="370.1" y1="186.7" x2="370.1" y2="214.3"/>
 
-
<g>
 
-
<polygon points="370.1,218.3 367.8,212.7 370.1,214 372.4,212.7 "/>
 
-
</g>
 
-
</g>
 
-
</g>
 
-
<g>
 
-
<g>
 
-
<line fill="none" stroke="#000000" stroke-width="1.1315" stroke-miterlimit="10" x1="472.3" y1="620.1" x2="472.3" y2="647.7"/>
 
-
<g>
 
-
<polygon points="472.3,651.7 470,646.1 472.3,647.4 474.6,646.1 "/>
 
-
</g>
 
-
</g>
 
-
</g>
 
-
<g>
 
-
<g>
 
-
<line fill="none" stroke="#000000" stroke-width="1.1315" stroke-miterlimit="10" x1="494" y1="620.1" x2="494" y2="647.7"/>
 
-
<g>
 
-
<polygon points="494,651.7 491.7,646.1 494,647.4 496.3,646.1 "/>
 
-
</g>
 
-
</g>
 
-
</g>
 
-
<text transform="matrix(1 0 0 1 376.3335 -15)" font-family="'MyriadPro-Regular'" font-size="12">AHL</text>
 
-
<text transform="matrix(1 0 0 1 593.3335 -15.1667)" font-family="'MyriadPro-Regular'" font-size="12">PAI2</text>
 
-
<text transform="matrix(1 0 0 1 375.3335 204.3333)" font-family="'MyriadPro-Regular'" font-size="12">Bxb1</text>
 
-
<text transform="matrix(1 0 0 1 595.3335 204.3332)" font-family="'MyriadPro-Regular'" font-size="12">ΦC31</text>
 
-
<text transform="matrix(1 0 0 1 396.3335 427.3333)"><tspan x="0" y="0" font-family="'MyriadPro-Regular'" font-size="12">SA</tspan><tspan x="13.3" y="0" font-family="'MyriadPro-Regular'" font-size="6">Bxb1</tspan></text>
 
-
<text transform="matrix(1 0 0 1 537.6668 429)"><tspan x="0" y="0" font-family="'MyriadPro-Regular'" font-size="12">SA</tspan><tspan x="13.3" y="0" font-family="'MyriadPro-Regular'" font-size="6">ΦC31</tspan></text>
 
-
<text transform="matrix(1 0 0 1 442.0002 639)" font-family="'MyriadPro-Regular'" font-size="12">GFP</text>
 
-
<text transform="matrix(1 0 0 1 502.0002 639)" font-family="'MyriadPro-Regular'" font-size="12">LuxI</text>
 
-
</svg>
 
-
-->
 
-
</article></html>
+
 
 +
function onWindowResize()
 +
{
 +
  var curWidth = $(window).width(),
 +
  curHeight = $(window).height(),
 +
  checking=false;
 +
  if (checking) {
 +
      return;
 +
  }
 +
  checking = true;
 +
  window.setTimeout(
 +
    function() {
 +
        var newWidth = $(window).width(),
 +
            newHeight = $(window).height();
 +
        if (!(newWidth !== curWidth ||
 +
            newHeight !== curHeight)) {
 +
            resize(false);
 +
        }
 +
        checking=false;
 +
    }, 300);
 +
}
 +
 
 +
function resize(initial) {
 +
if (!initial)
 +
{
 +
    var container =  $('#article');
 +
    var imgWidth = container.width();
 +
 
 +
  $( "#map" ).each(function() {
 +
      $(this).css('height', 'auto', 'width', 'auto');
 +
      $(this).mapster('resize',Math.min(imgWidth, $(this).naturalWidth()) ,0,0); 
 +
  });
 +
}
 +
 
 +
}
 +
 
 +
 
 +
$(document).ready(function(){
 +
 
 +
$('#map').mapster({
 +
    fillOpacity: 0.5,
 +
    isSelectable: false,
 +
    clickNavigate: true,
 +
    mapKey: 'name',
 +
    areas: [
 +
            {
 +
                key: "qs",
 +
                fillColor: '2C2F3D'
 +
            },
 +
 
 +
            {
 +
                key: "integrases",
 +
                fillColor: '2C2F3D'
 +
            },
 +
 
 +
            {
 +
                key: "xor",
 +
                fillColor: '2C2F3D'
 +
            },
 +
 
 +
            {
 +
                key: "diff",
 +
                fillColor: '2C2F3D'
 +
            },
 +
 
 +
            {
 +
                key: "cell",
 +
                fillColor: 'FFFFFF'
 +
            }
 +
            ]
 +
  });
 +
 
 +
 
 +
 
 +
 
 +
$(window).resize(
 +
  function()
 +
  {
 +
onWindowResize();
 +
  });
 +
resize(true);
 +
});
 +
</script>
 +
 
 +
<article id="article">
 +
<center>
 +
Our whole model is the result of separate studies for every module of the system. We started with mass action kinetics to model the reactions of all modules, and chose the proper approximations to fit parameters when they were unknown.
 +
The flow of the information is characterized by transfer functions. Click on the different modules to check out their precise characterization. For a global description of the whole cell model as a black box, click on Whole cell model.
 +
</center>
 +
<br/>
 +
<br/>
 +
<center>
 +
<img usemap="#map" id="map" src="/wiki/images/1/11/ETH_Zurich_Modeling-overview.png" style="width:100%;"/>
 +
<map id="map" name="map"><area shape="rect" alt="" title="Diffusion model" coords="448,1,642,185" href="https://2014.igem.org/Team:ETH_Zurich/modeling/diffmodel" target="" name='diff' /><area shape="rect" name='qs' alt="" title="Quorum sensing module" coords="636,349,997,799" href="https://2014.igem.org/Team:ETH_Zurich/modeling/qs" target="" /><area shape="rect" name='integrases' alt="" title="Integrase module" coords="97,889,457,1339" href="https://2014.igem.org/Team:ETH_Zurich/modeling/int" target="" /><area name='qs' shape="rect" alt="" title="Quorum sensing module" coords="97,349,456,798" href="https://2014.igem.org/Team:ETH_Zurich/modeling/qs" target="" /><area name='integrases' shape="rect" alt="" title="Integrase module" coords="636,889,997,1338" href="https://2014.igem.org/Team:ETH_Zurich/modeling/int" target="" /><area shape="rect" name='xor' alt="" title="Xor gate module" coords="325,1446,770,1866" href="https://2014.igem.org/Team:ETH_Zurich/modeling/xor" target="" /><area name='cell' shape="rect" alt="" title="Whole cell model" coords="1,301,61,2037" href="https://2014.igem.org/Team:ETH_Zurich/modeling/whole" target="" /><!-- Created by Online Image Map Editor (http://www.maschek.hu/imagemap/index) --></map>
 +
 
 +
</center>
 +
 
 +
 
 +
</article>
 +
 
 +
 
 +
</html>
{{:Team:ETH Zurich/tpl/foot}}
{{:Team:ETH Zurich/tpl/foot}}

Latest revision as of 00:15, 18 October 2014

iGEM ETH Zurich 2014