Latest revision as of 03:44, 18 October 2014

Modelling Homepage

Our team believes that the key to synthetic biology is to use engineering-based models and designs to improve the development of biochemical systems. Therefore, the engineers in our team have worked with the biochemists every step of the way to design initial project ideas, analyse in detail the expected response of the system, and interpret the results of the various types of experiments that we have run.

This means that, unlike some teams in the past, our modelling is interspersed with our biochemistry information to give a feel of the real interactions that have taken place between the specialities in our team. To aid the viewer, all modelling sections have pink header bubbles, all of the biochemistry sections have light blue header bubbles.

We have also worked very closely with the policy and practices team and influential figures in industry to look at exactly how this project could be implemented in the real world. Included in this has been the 3D CAD (computer aided design) of the expected product and the 3D printing and circuit building of the biosensor unit.

Click on the links below to find out more!

Characterising a genetic network
We used stochastic and deterministic genetic circuit modelling to help the wet-lab team in characterising a previously unknown genetic circuit. Find out more here...

Optimising a genetic network
We used these genetic circuit models to predict the fluoresence of the system as a response to thousands of different combinations of inputs. This allowed us to optimise the input levels and advise the biochemists on the construction of the system so that we could develop the best possible system in the amount of time available. See what we found out...

Analysing the native bacterium
We constructed a model based on Michaelis-Menten kinetics that could inform us how much DCM the native bacterium would be able to degrade and also what the pH change of the system would be. This further convinced us to use synthetic biology to solve the problem of chlorinated waste disposal. See how we did it here...

Analysing microcompartments mathematically
We used spacial modelling to determine an estimate of various parameters to do with the microcompartments. We then gave this information to the biochemists to help them analyse their results with expressing microcompartments in E. coli and P. putida.

Analysing the benefits of microcompartments
On this page we explain in detail how our stochastic diffusion models work and then provide in-depth information on how we then used these carefully analyse of the benefits of microcompartments for our system.

Creating models of iGEM Melbourne's star peptide
We embarked on a major collaboration project with Melbourne iGEM team. Part of this collaboration involved helping this team by modelling the benefit of using their star peptide system in a bacterium and how that could control reaction rates. To do this we drew on the extensive knowledge that we have gained of stochastically modelling diffusion-driven systems.

Realising the biosensor
On the advice of industry experts, we produced concept designs of our whole system using CAD. We built the biosensor using the latest 3D printing technologies and we designed and built a very cheap circuit that can detect low levels of GFP fluorescence to go inside the biosensor. This part is really exciting...

Bioremediation realisation
Discover how we envisage our project becoming a real world product and see the CAD models that have allowed us to demonstrate our idea to industry experts.

Biopolymer containment
Find out how we modelled the processes that control the diffusion of DCM and reaction products through the biopolymer containment beads, and how this modelling played an integral part in calculating the optimum bead thickness for our system.

@@ Line 1: / Line 1: @@
+{{Team:Oxford/templates/header}}
 <html>
-<head>
-  <style type="text/css">
-  @import url(http://fonts.googleapis.com/css?family=PT+Serif|Open+Sans:300italic,400,300);
-  html, body {
-    max-width: 100%;
-    overflow-x: hidden;
-  }
-  body {
-    background-color: #EBEBEB;
-    margin: 0px;
-    padding: 0;
-    border: 0;
-    vertical-align: baseline;
-    font-family: 'Open Sans', 'helvetica', sans-serif;
-    font-size: 10px;
-    font-weight: 300;
-  }
-  #content {
-    border:none;
-    width:100%;
-    margin:0;
-    padding:0;
-    background:none;
-  }
-  #catlinks {
-    display:none;
-  }
-  #contentSub {
-    display:none;
-  }
-  #menubar {
-    width: auto;
-    margin-top:0.5%;
-}
-  .left-menu:hover {
-    background-color: transparent;
-  }
-  #menubar li a {
-    background-color: transparent;
-  }
-  #menubar:hover {
-    color: gray;
-  }
-  #menubar li a {
-    color: #B5B5B5;
-  }
-  #menubar:hover li a {
-    color: gray;
-  }
-  #menubar.left-menu.noprint ul li:last-child {
-   display:none;
-  }
-  #search-controls {
-    display:none;
-  }
-  #top-section {
-    height:0px;
-    width:100%;
-    border:none;
-  }
-  #footer-box {
-    border:none;
-    display:none;
-    width:100%;
-  }
-  #p-logo {
-    display:none
-  }
-  .firstHeading {
-  display:none;
-  }
-  #bodyContent p{
-    display:none;
-  }
-  html, div, span, applet, object, iframe,
-  h1, h2, h3, h4, h5, h6, p, blockquote, pre,
-  a, abbr, acronym, address, big, cite, code,
-  del, dfn, em, img, ins, kbd, q, s, samp,
-  small, strike, strong, sub, sup, tt, var,
-  b, u, i, center,
-  dl, dt, dd, ol, ul, li,
-  fieldset, form, label, legend,
-  table, caption, tbody, tfoot, thead, tr, th, td,
-  article, aside, canvas, details, embed,
-  figure, figcaption, footer, header, hgroup,
-  menu, nav, output, ruby, section, summary,
-  time, mark, audio, video {
-    margin: 0;
-    padding: 0;
-    border: 0;
-    font-size: 100%;
-    font: inherit;
-    vertical-align: baseline;
-  }
-  #top-section {
-    width: 965px;
-    height: 0;
-    margin: 0 auto;
-    padding: 0;
-    border: none;}
-  .left-menu:hover {
-    background-color: transparent;}
-  #menubar li a {
-    background-color: transparent;}
-  .outer {
-    position:fixed;
-    width:100%;
-    height:100%;
-  }
-  img.supercoil {
-    width:65%;
-    display: block;
-    margin-left: auto;
-    margin-right: auto }
-  .Heading {
-    position:absolute;
-    display: block;
-  }
-.heading {
-    -webkit-transition: margin-left 0.3s, -webkit-transform 0.3s;
-    transition: margin-left 0.3s;
-}
-.heading:hover {
-    margin-left:30px;
-}
-.pink_news_block {
-        background: #FDDBDB;
-        border-radius:15px; margin-top:2%; padding-left:2%;padding-right:2%;padding-top:3%;padding-bottom:3%;
-width:96%;
-}
-.right_news_block {
-        background: #fff;
-        border-radius:15px; padding-left:2%;padding-right:2%;padding-top:3%;padding-bottom:3%;
-width:75%;float:right;line-height:150%;
-}
-.right_news_block2 {
-        background: #fff;
-        border-radius:15px; padding-left:2%;padding-right:2%;padding-top:3%;padding-bottom:3%;
-width:75%;float:right;line-height:150%;margin-top:2%;
-}
-.blue_news_block {
-        background: #ADD8E6;
-        border-radius:15px; margin-top:2%; padding-left:2%;padding-right:2%;padding-top:3%;padding-bottom:3%;
-width:96%;
-}
-.orange_news_block1 {
-        background: #FA6800;
-        border-radius:30px; margin-top:2%; padding-left:2%;padding-right:2%;padding-top:2%;padding-bottom:2%;
-width:32%;
-}
-.orange_news_block2 {
-        background: #FA6800;
-        border-radius:30px; margin-top:2%; padding-left:2%;padding-right:2%;padding-top:2%;padding-bottom:2%;
-width:96%;
-}
-.yellow_news_block {
-        background: #FFFF06;
-        border-radius:30px; margin-top:2%; padding-left:2%;padding-right:2%;padding-top:2%;padding-bottom:2%;
-width:27%;
-}
-.white_news_block {
-        background: #fff;
-        border-radius:15px; margin-top:2%; margin-left: 0%; padding-left:2%;padding-right:2%;padding-top:2%;padding-bottom:2%;
-width:96%;
-}
-h1 {
-	font-size: 120%;
-	font-weight: 400;
-	font-family:Helvetica;
-	margin-bottom: 2%;
-        line-height:150%;
-}
-h1white {
-	font-size: 230%;
-	font-weight: 400;
-	font-family:Helvetica;
-        color:#fff;
-        line-height:150%;
-}
-h1blue {
-	font-size: 180%;
-	font-weight: 400;
-	font-family:Helvetica;
-        color:#4747E5;
-        line-height:150%;
-        font-style: italic;
-}
-h1blue2 {
-	font-size: 130%;
-	font-weight: 400;
-	font-family:Helvetica;
-        color:#4747E5;
-        line-height:150%;
-}
-h1blue3 {
-	font-size: 140%;
-	font-weight: 400;
-	font-family:Helvetica;
-        color:#4747E5;
-        line-height:150%;
-}
-h2blue3 {
-	font-size: 120%;
-	font-weight: 400;
-	font-family:Helvetica;
-        color:#4747E5;
-        line-height:150%;
-}
-h1black {
-	font-size: 230%;
-	font-weight: 400;
-	font-family:Helvetica;
-        line-height:150%;
-}
-h1grey {
-	font-size: 280%;
-	font-weight: 400;
-	font-family:Helvetica;
-        color:#615555;
-        line-height:150%;
-}
-h1purple {
-	font-size: 140%;
-	font-weight: 400;
-	font-family:Helvetica;
-        color:#CE68D5;
-        line-height:150%;
-}
-h2purple {
-	font-size: 120%;
-	font-weight: 400;
-	font-family:Helvetica;
-        color:#CE68D5;
-        line-height:150%;
-}
-h1red {
-	font-size: 140%;
-	font-weight: 400;
-	font-family:Helvetica;
-        color:#B31127;
-        line-height:150%;
-}
-h2red {
-	font-size: 120%;
-	font-weight: 400;
-	font-family:Helvetica;
-        color:#B31127;
-        line-height:150%;
-}
-h1orange {
-	font-size: 140%;
-	font-weight: 400;
-	font-family:Helvetica;
-        color:#F98500;
-        line-height:150%;
-}
-h2orange {
-	font-size: 120%;
-	font-weight: 400;
-	font-family:Helvetica;
-        color:#F98500;
-        line-height:150%;
-}
-h1green {
-	font-size: 140%;
-	font-weight: 400;
-	font-family:Helvetica;
-        color:#0F9101;
-        line-height:150%;
-}
-h2green {
-	font-size: 120%;
-	font-weight: 400;
-	font-family:Helvetica;
-        color:#0F9101;
-        line-height:150%;
-}
-  </style>
-   #list li {
-list-style-image: url("https://static.igem.org/mediawiki/2014/6/6f/OxigemTick.png"); }
-}
-  </style>
-  <script type="text/javascript">
-  function iconleft(x) {
-    x.style.left="6%";
-  }
-  function iconnormal(x) {
-    x.style.left="9%";
-  }
-$(document).ready(function(){
-  $("#arrowr").click(function(){
-    $("#grey").animate({right:'-175px'}, "fast");
-  });
-  $("#arrowl").click(function(){
-    $("#grey").animate({right:'-120px'}, "fast");
-  });
-  $("#modelling").hover(function(){
-    $("#modelling").animate({opacity:'0.95'}, "fast");
-    $("#modelling1").css({display:'inline'});
-  });
-  $("#modelling").mouseout(function(){
-    $("#modelling").animate({opacity:'0.75'}, "fast");
-    $("#modelling1").css({display:'none'});
-  });
-  $("#achievements").hover(function(){
-    $("#achievements").animate({opacity:'0.95'}, "fast");
-    $("#achievements1").css({display:'inline'});
-  });
-  $("#achievements").mouseout(function(){
-    $("#achievements").animate({opacity:'0.75'}, "fast");
-    $("#achievements1").css({display:'none'});
-  });
-  $("#igemcomm").hover(function(){
-    $("#igemcomm").animate({opacity:'0.95'}, "fast");
-    $("#igemcomm1").css({display:'inline'});
-  });
-  $("#igemcomm").mouseout(function(){
-    $("#igemcomm").animate({opacity:'0.75'}, "fast");
-    $("#igemcomm1").css({display:'none'});
-  });
-  $("#safety").hover(function(){
-    $("#safety").animate({opacity:'0.95'}, "fast");
-    $("#safety1").css({display:'inline'});
-  });
-  $("#safety").mouseout(function(){
-    $("#safety").animate({opacity:'0.75'}, "fast");
-    $("#safety1").css({display:'none'});
-  });
-  $("#team").hover(function(){
-    $("#team").animate({opacity:'0.95'}, "fast");
-    $("#team1").css({display:'inline'});
-  });
-  $("#team").mouseout(function(){
-    $("#team").animate({opacity:'0.75'}, "fast");
-    $("#team1").css({display:'none'});
-  });
-  $("#dcmation").hover(function(){
-    $("#dcmation").animate({opacity:'0.95'}, "fast");
-    $("#dcmation1").css({display:'inline'});
-  });
-  $("#dcmation").mouseout(function(){
-    $("#dcmation").animate({opacity:'0.75'}, "fast");
-    $("#dcmation1").css({display:'none'});
-  });
-  $("#interlab").hover(function(){
-    $("#interlab").animate({opacity:'0.95'}, "fast");
-    $("#interlab1").css({display:'inline'});
-  });
-  $("#interlab").mouseout(function(){
-    $("#interlab").animate({opacity:'0.75'}, "fast");
-    $("#interlab1").css({display:'none'});
-  });
-  $("#policy").hover(function(){
-    $("#policy").animate({opacity:'0.95'}, "fast");
-    $("#policy1").css({display:'inline'});
-  });
-  $("#policy").mouseout(function(){
-    $("#policy").animate({opacity:'0.75'}, "fast");
-    $("#policy1").css({display:'none'});
-  });
-});
-jQuery(document).ready(function(){
-    jQuery('#tb1').live('click', function(event) {
-         jQuery('#b1').toggle('show');
-    });
-    jQuery('#tb2').live('click', function(event) {
-         jQuery('#b2').toggle('show');
-    });
-    jQuery('#tb3').live('click', function(event) {
-         jQuery('#b3').toggle('show');
-    });
-    jQuery('#tb4').live('click', function(event) {
-         jQuery('#b4').toggle('show');
-    });
-    jQuery('#tb5').live('click', function(event) {
-         jQuery('#b5').toggle('show');
-    });
-    jQuery('#ts1').live('click', function(event) {
-         jQuery('#s1').toggle('show');
-    });
-    jQuery('#ts2').live('click', function(event) {
-         jQuery('#s2').toggle('show');
-    });
-    jQuery('#ts3').live('click', function(event) {
-         jQuery('#s3').toggle('show');
-    });
-    jQuery('#ts4').live('click', function(event) {
-         jQuery('#s4').toggle('show');
-    });
-    jQuery('#tg1').live('click', function(event) {
-         jQuery('#g1').toggle('show');
-    });
-    jQuery('#tg2').live('click', function(event) {
-         jQuery('#g2').toggle('show');
-    });
-    jQuery('#tg3').live('click', function(event) {
-         jQuery('#g3').toggle('show');
-    });
-});
-function startup(){
-  $("#sidebarblue").animate({marginLeft:'+=250px'}, 1000);
-  $("#sidebarlogo").animate({marginLeft:'+=250px'}, 1000);
-}
-function startup1(){
-  $(".1").animate({marginLeft:'+=250px'}, 1000);
-}
-function startup2(){
-  $(".2").animate({marginLeft:'+=250px'}, 1000);
-}
-function startup3(){
-  $(".3").animate({marginLeft:'+=250px'}, 1000);
-}
-function startup4(){
-  $(".4").animate({marginLeft:'+=250px'}, 1000);
-}
-$(document).ready(function(){
-  setTimeout(function() {
-    startup();
-  }, 1500);
-  setTimeout(function() {
-    startup1();
-  }, 1520);
-  setTimeout(function() {
-    startup2();
-  }, 1560);
-  setTimeout(function() {
-    startup3();
-  }, 1640);
-  setTimeout(function() {
-    startup4();
-  }, 1750);
-});
-  </script>
-  <title></title>
-</head>
 <body>
    <div class="outer" style="overflow-y: scroll; overflow-x: hidden;">
+<div id="stuff" style="float:left;position:absolute;margin-left:200px;margin-right:100px; margin-top:50px;min-width:645px;">
+<img src="https://static.igem.org/mediawiki/2014/4/44/MattBoothStochasticNormal2.png" style="position:absolute; width:100%;z-index:-1; border-radius:15px;"/>
-<div id="stuff" style="float:left;position:absolute;margin-left:200px;margin-right:100px; margin-top:50px;">
+<div style="background-color:#D9D9D9; opacity:0.7; z-index:5; Height:75px; width:100%;font-size:65px;font-family:Helvetica;padding-top:5px;margin-top:10px; font-weight: 450;">
+<div style="background-color:white; opacity:0.7; Height:75px; width:100%;margin-top:5px:margin-bottom:5px;font-size:65px;font-family:Helvetica;padding-top:5px; color:#00000; font-weight: 450;"><br><center><font style="opacity:0.7">Modelling Homepage</font></center></div>
+</div>
+<br>
-<img src="https://static.igem.org/mediawiki/2014/0/08/Oxigemradcamcrop.jpg" style="position:absolute; width:100%;min-width:100%;z-index:-1; border-radius:15px;"/>
+<div style="border-bottom-left-radius:10px;border-bottom-right-radius:10px; padding-left:10px;padding-right:10px;min-width:300px;">
+<img src="https://static.igem.org/mediawiki/2014/e/e9/Oxford_Mod_hmpg.png" style="width:27%;margin-left:36.5%;margin-top:-20px;">
-<div style="background-color:#D9D9D9; opacity:0.7; z-index:5; margin-right:auto;margin-left:auto; Height:75px; width:80%;min-width:300px;font-size:65px;font-family:Helvetica;padding-top:5px; font-weight: 450;">
-<div style="background-color:white; opacity:0.7; Height:75px; width:100%;margin-top:5px:margin-bottom:5px;min-width:300px;font-size:65px;font-family:Helvetica;padding-top:5px; color:#596C8A; font-weight: 450;"><br>Modelling Homepage</div>
 </div>
-<br><br>
-<div class="white_news_block">
-<img src="https://static.igem.org/mediawiki/2014/8/8c/Homepage_Diagram.jpg" style="float:left;position:relative; width:21%;" />
+<div style="background-color:white; border-bottom-left-radius:10px;border-radius:10px; padding-left:10px;padding-right:10px;min-width:300px;margin-top:20px;">
+<br>
+</div>
+<br>
-<h1>Our team believes that the key to synthetic biology is using engineering design and engineering modelling to significantly improve the development of biochemical systems. Therefore, the engineers in our team have worked with the biochemists every step of the way throughout our project to design the initial project ideas, to analyse in detail the expected response of the system and to analyse the results of the various types of experiments that we have run.
+<div style="background-color:white; border-bottom-left-radius:10px;border-radius:10px; padding-left:10px;padding-right:10px;min-width:300px;margin-top:-35px;">
+<br>
+<h1 style="color:#777777">Our team believes that the key to synthetic biology is to use engineering-based models and designs to improve the development of biochemical systems. Therefore, the engineers in our team have worked with the biochemists every step of the way to design initial project ideas, analyse in detail the expected response of the system, and interpret the results of the various types of experiments that we have run.
 <br><br>
-This means that, unlike iGEM teams in the past, our modelling is presented interspersed with our biochemistry information to hopefully give a feel of the real interactions that have taken place between the specialities in our team. To aid the viewer, all modelling sections have pink header bubbles, all of the biochemistry sections have light blue header bubbles.
+This means that, unlike some teams in the past, our modelling is interspersed with our biochemistry information to give a feel of the real interactions that have taken place between the specialities in our team. To aid the viewer, all modelling sections have pink header bubbles, all of the biochemistry sections have light blue header bubbles.
 <br><br>
-We have also worked very closely with the human practices team and influential figures in industry to look at exactly how this project could be implemented in the real world. Included in this has been the 3D CAD of the expected product and the 3D printing and circuit building of the biosensor unit.
+We have also worked very closely with the policy and practices team and influential figures in industry to look at exactly how this project could be implemented in the real world. Included in this has been the 3D CAD (computer aided design) of the expected product and the 3D printing and circuit building of the biosensor unit.
 <br><br>
-Click on the links below to find out more.</h1>
+Click on the links below to find out more!</h1>
+<br>
 </div>
@@ Line 554: / Line 45: @@
-<a href="https://2014.igem.org/Team:Oxford/P&P_environmental_impact"><div class="white_news_block">
+<a href="https://2014.igem.org/Team:Oxford/biosensor_characterisation#showmodelling"><div style="background-color:white; border-bottom-left-radius:10px;border-radius:10px; padding-left:10px;padding-right:10px;min-width:300px;margin-top:15px;">
-<img src="https://static.igem.org/mediawiki/2014/1/19/Oxford_Environment.png" style="float:left;position:relative; width:6%;margin-right:3%;" />
+<img src="https://static.igem.org/mediawiki/2014/0/0d/Oxford_q2.png" style="float:left;position:relative; width:6%;margin-right:3%;" />
+<br>
 <h1blue3>Characterising a genetic network</h1blue3>
 <br>
-<h2blue3>We used stochastic and deterministic genetic circuit modelling helped the wet-lab team develop the ability to characterise a previously unknown genetic circuit. Find out more here...
+<h2blue3>We used stochastic and deterministic genetic circuit modelling to help the wet-lab team in characterising a previously unknown genetic circuit. Find out more here...
 </h2blue3>
+<br><br>
 </div></a>
@@ Line 569: / Line 61: @@
-<a href="https://2014.igem.org/Team:Oxford/P&P_environmental_impact"><div class="white_news_block">
+<a href="https://2014.igem.org/Team:Oxford/biosensor_optimisation#showmodelling"><div style="background-color:white; border-bottom-left-radius:10px;border-radius:10px; padding-left:10px;padding-right:10px;min-width:300px;margin-top:15px;">
 <img src="https://static.igem.org/mediawiki/2014/4/43/Oxford_Realisation2.png" style="float:right;position:relative; width:6%;margin-right:3%;" />
+<br>
-<h1red>Practicality….</h1red>
+<h1red>Optimising a genetic network</h1red>
 <br>
-<h2red>How can the idea be implemented and delivered in the real world? Our engineers used design software and 3D printing to think about how we might realise DCMation and the environments in which the biosensor and bioremediation technique might be used.</h2red>
+<h2red>We used these genetic circuit models to predict the fluoresence of the system as a response to thousands of different combinations of inputs. This allowed us to optimise the input levels and advise the biochemists on the construction of the system so that we could develop the best possible system in the amount of time available. See what we found out...</h2red>
+<br><br>
 </div></a>
@@ Line 591: / Line 83: @@
-<a href="https://2014.igem.org/Team:Oxford/P&P_intellectual_property"><div class="white_news_block">
+<a href="https://2014.igem.org/Team:Oxford/how_much_can_we_degrade?#showmodelling"><div style="background-color:white; border-bottom-left-radius:10px;border-radius:10px; padding-left:10px;padding-right:10px;min-width:300px;margin-top:15px;">
-<img src="https://static.igem.org/mediawiki/2014/c/c7/Oxford_IP.png" style="float:left;position:relative; width:6%;margin-right:3%;" />
+<img src="https://static.igem.org/mediawiki/2014/6/65/Oxford_dm4_.png" style="float:left;position:relative; width:6%;margin-right:3%;" />
+<br>
-<h1purple>Intellectual Property….</h1purple>
+<h1purple>Analysing the native bacterium</h1purple>
 <br>
-<h2purple>Determining the ownership of the intellectual property of a project is crucial for any team hoping to develop their ideas beyond the Jamboree. Our report looks at how the iGEM community can navigate this controversial and difficult issue. </h2purple>
+<h2purple>We constructed a model based on Michaelis-Menten kinetics that could inform us how much DCM the native bacterium would be able to degrade and also what the pH change of the system would be. This further convinced us to use synthetic biology to solve the problem of chlorinated waste disposal. See how we did it here...</h2purple>
+<br><br>
 </div></a>
@@ Line 611: / Line 103: @@
-<a href="https://2014.igem.org/Team:Oxford/P&P_communication"><div class="white_news_block">
+<a href="https://2014.igem.org/Team:Oxford/what_are_microcompartments?#showmodelling"><div style="background-color:white; border-bottom-left-radius:10px;border-radius:10px; padding-left:10px;padding-right:10px;min-width:300px;margin-top:15px;">
-<img src="https://static.igem.org/mediawiki/2014/c/c5/Oxford_Communication.png" style="float:right;position:relative; width:10%;margin-right:3%;" />
+<img src="https://static.igem.org/mediawiki/2014/2/27/Oxford_q.png" style="float:right;position:relative; width:10%;margin-right:3%;" />
+<br>
-<h1orange>Communication….</h1orange>
+<h1orange>Analysing microcompartments mathematically</h1orange>
 <br>
-<h2orange>Determining the ownership of the intellectual property of a project is crucial for any team hoping to develop their ideas beyond the Jamboree. Our report looks at how the iGEM community can navigate this controversial and difficult issue. </h2orange>
+<h2orange>We used spacial modelling to determine an estimate of various parameters to do with the microcompartments. We then gave this information to the biochemists to help them analyse their results with expressing microcompartments in E. coli and P. putida.</h2orange>
+<br><br>
 </div></a>
@@ Line 630: / Line 122: @@
-<a href="https://2014.igem.org/Team:Oxford/P&P_public_engagement"><div class="white_news_block">
+<a href="https://2014.igem.org/Team:Oxford/why_do_we_need_microcompartments?#showmodelling"><div style="background-color:white; border-bottom-left-radius:10px;border-radius:10px; padding-left:10px;padding-right:10px;min-width:300px;margin-top:15px;">
-<img src="https://static.igem.org/mediawiki/2014/c/c6/Oxford_public.png" style="float:left;position:relative; width:6%;margin-right:3%;" />
+<img src="https://static.igem.org/mediawiki/2014/6/6f/Oxford_analyse_micro2.png" style="float:left;position:relative; width:10%;margin-right:3%;" />
+<br>
-<h1blue3>Public Participation….</h1blue3>
+<h1blue3>Analysing the benefits of microcompartments</h1blue3>
 <br>
 <h2blue3>
-Determining the ownership of the intellectual property of a project is crucial for any team hoping to develop their ideas beyond the Jamboree. Our report looks at how the iGEM community can navigate this controversial and difficult issue.
+On this page we explain in detail how our stochastic diffusion models work and then provide in-depth information on how we then used these carefully analyse of the benefits of microcompartments for our system.
 </h2blue3>
+<br><br>
 </div></a>
@@ Line 654: / Line 146: @@
-<a href="https://2014.igem.org/Team:Oxford/P&P_igem_europe"><div class="white_news_block">
+<a href="https://2014.igem.org/Team:Oxford/alternatives_to_microcompartments#showmodelling"><div style="background-color:white; border-bottom-left-radius:10px;border-radius:10px; padding-left:10px;padding-right:10px;min-width:300px;margin-top:15px;">
-<img src="https://static.igem.org/mediawiki/2014/e/e5/Oxford_europe.png" style="float:right;position:relative; width:10%;margin-right:3%;" />
+<img src="https://static.igem.org/mediawiki/2014/2/20/Oxford_shake.png" style="float:right;position:relative; width:10%;margin-right:3%;" />
+<br>
-<h1green>The iGEM Competition….</h1green>
+<h1green>Creating models of iGEM Melbourne's star peptide </h1green>
 <br>
 <h2green>
-iGEM has been steadily expanding since its beginnings in 2004, climbing from 5 to over 200 teams in the last 10 years. As the first ever Oxford team, we are more than a little late to the party! Our team has researched the growing contribution made by the rest of Europe to the competition, of which we hope to become a part from 2014 onwards!
+We embarked on a major collaboration project with Melbourne iGEM team. Part of this collaboration involved helping this team by modelling the benefit of using their star peptide system in a bacterium and how that could control reaction rates. To do this we drew on the extensive knowledge that we have gained of stochastically modelling diffusion-driven systems.
 </h2green>
+<br><br>
 </div></a>
@@ Line 677: / Line 169: @@
+<a href="https://2014.igem.org/Team:Oxford/biosensor_realisation#showmodelling"><div style="background-color:white; border-bottom-left-radius:10px;border-radius:10px; padding-left:10px;padding-right:10px;min-width:300px;margin-top:15px;">
+<img src="https://static.igem.org/mediawiki/2014/4/43/Oxford_Realisation2.png" style="float:left;position:relative; width:6%;margin-right:3%;" />
+<br>
+<h1red>Realising the biosensor</h1red>
+<br>
+<h2red>On the advice of industry experts, we produced concept designs of our whole system using CAD. We built the biosensor using the latest 3D printing technologies and we designed and built a very cheap circuit that can detect low levels of GFP fluorescence to go inside the biosensor. This part is really exciting...</h2red>
+<br><br>
+</div></a>
@@ Line 689: / Line 189: @@
+<a href="https://2014.igem.org/Team:Oxford/realisation_bioremediation#showmodelling"><div style="background-color:white; border-bottom-left-radius:10px;border-radius:10px; padding-left:10px;padding-right:10px;min-width:300px;margin-top:15px;">
+<img src="https://static.igem.org/mediawiki/2014/4/43/Oxford_Realisation2.png" style="float:right;position:relative; width:6%;margin-right:3%;" />
+<br>
+<h1orange>Bioremediation realisation</h1orange>
+<br>
+<h2orange> Discover how we envisage our project becoming a real world product and see the CAD models that have allowed us to demonstrate our idea to industry experts.</h2orange>
+<br><br>
+</div></a>
@@ Line 706: / Line 214: @@
+<a href="https://2014.igem.org/Team:Oxford/biopolymer_containment#showmodelling"><div style="background-color:white; border-bottom-left-radius:10px;border-radius:10px; padding-left:10px;padding-right:10px;min-width:300px;margin-top:15px;">
+<img src="https://static.igem.org/mediawiki/2014/4/43/Oxford_Realisation2.png" style="float:left;position:relative; width:6%;margin-right:3%;" />
+<br>
+<h1blue3>Biopolymer containment</h1blue3>
+<br>
+<h2blue3> Find out how we modelled the processes that control the diffusion of DCM and reaction products through the biopolymer containment beads, and how this modelling played an integral part in calculating the optimum bead thickness for our system.</h2blue3>
+<br><br>
+</div></a>
+<br>
-<div class="white_news_block">
-<a href="https://2014.igem.org/Team:Oxford/policy_and_practices">
-<img src="https://static.igem.org/mediawiki/2014/3/33/Oxford_P%26P1.png" style="float:left;position:relative; width:12%;" /></a>
-<a href="https://2014.igem.org/Team:Oxford/P&P_environmental_impact"><img src="https://static.igem.org/mediawiki/2014/7/75/Oxford_P%26P2.png" style="float:left;position:relative; width:12%; margin-left:2.66%;" /></a>
-<a href="https://2014.igem.org/Team:Oxford/P&P_environmental_impact"><img src="https://static.igem.org/mediawiki/2014/3/3f/Oxford_P%26P3.png" style="float:left;position:relative; width:12%; margin-left: 2.66%" /></a>
-<a href="https://2014.igem.org/Team:Oxford/P&P_intellectual_property"><img src="https://static.igem.org/mediawiki/2014/0/00/Oxford_P%26P4.png" style="float:left;position:relative; width:12%;margin-left: 2.66%;" /></a>
-<a href="https://2014.igem.org/Team:Oxford/P&P_communication">
-<img src="https://static.igem.org/mediawiki/2014/4/43/Oxford_P%26P5.png" style="float:left;position:relative; width:13%; margin-left: 2.5%" /></a>
-<a href="https://2014.igem.org/Team:Oxford/P&P_public_engagement"><img src="https://static.igem.org/mediawiki/2014/3/32/Oxford_P%26P6.png" style="float:left;position:relative; width:12%; margin-left: 2.66%;" /></a>
-<a href="https://2014.igem.org/Team:Oxford/P&P_igem_europe">
-<img src="https://static.igem.org/mediawiki/2014/9/92/Oxford_P%26P7.png" style="float:right;position:relative; width:12%;" /></a>
-<br><br><br><br><br><br><br><br><br>
-</div>
-</div>
-<div id="sponsors" style="height:10%; width:100%;"></div>
-</div>
-<img id="sidebarblue" src="https://static.igem.org/mediawiki/2014/e/ec/OxigemsidebarBlue.png" style="float:left;position:fixed;margin-left:-250px;height:100%;" />
-<img class="1" src="https://static.igem.org/mediawiki/2014/a/a5/OxigemDotsDCMation.png" style="opacity:0.9;float:left;position:fixed;margin-left:-250px; top:31.6%; height:17.6%;" />
-<img class="2" src="https://static.igem.org/mediawiki/2014/0/06/OxigemDotsinterlab.png" style="opacity:0.9;float:left;position:fixed;margin-left:-250px; top:18.3%; height:15.125%;" />
-<img class="3" src="https://static.igem.org/mediawiki/2014/e/ee/OxigemDotsP%26P.png" style="opacity:0.9;float:left;position:fixed;margin-left:-250px; top:9%; height:12.75%;" />
-<img class="4" src="https://static.igem.org/mediawiki/2014/c/ca/OxigemDotsTeam.png" style="float:left;position:fixed;margin-left:-250px; top:0%; height:12.625%;" />
-<img class="1" src="https://static.igem.org/mediawiki/2014/f/f5/OxigemDotsModelling.png" style="opacity:0.8;float:left;position:fixed;margin-left:-250px; top:50.6%; height:17.75%;" />
-<img class="2" src="https://static.igem.org/mediawiki/2014/8/87/OxigemDotsAchievements.png" style="opacity:0.9;float:left;position:fixed;margin-left:-250px; top:66.45%; height:13.28%;" />
-<img class="3" src="https://static.igem.org/mediawiki/2014/7/7b/OxigemDotsiGEMcomm.png" style="opacity:0.9;float:left;position:fixed;margin-left:-250px; top:78%; height:12.5%;" />
-<img class="4" src="https://static.igem.org/mediawiki/2014/0/0e/OxigemDotsSafety.png" style="float:left;position:fixed;margin-left:-250px; top:88.15%; height:11.9%;" />
-<a href="https://2014.igem.org/Team:Oxford"><img id="sidebarlogo" class="oxigem" src="https://static.igem.org/mediawiki/2014/a/a4/Oxigemsidebarlogo.png" style="float:left;position:fixed;margin-left:-250px; top:42.5%; height:15%;"/></a>
-<img src="https://static.igem.org/mediawiki/2014/3/37/OxigemDotModelling.png" style="float:left;position:fixed; top:59.3%; height:4.125%;" />
-<img src="https://static.igem.org/mediawiki/2014/0/05/OxigemDotAchievements.png" style="float:left;position:fixed; top:71%; height:4%;" />
-<img src="https://static.igem.org/mediawiki/2014/7/77/OxigemDotiGEMcomm.png" style="float:left;position:fixed; top:81.5%; height:4.375%;" />
-<img src="https://static.igem.org/mediawiki/2014/2/27/OxigemDotSafety.png" style="float:left;position:fixed; top:93%; height:4.125%;" />
-<img src="https://static.igem.org/mediawiki/2014/e/e7/OxigemDotDCMation.png" style="float:left;position:fixed; top:37%; height:4.125%;" />
-<img src="https://static.igem.org/mediawiki/2014/9/94/OxigemDotInterlab.png" style="float:left;position:fixed; top:25%; height:4.125%;" />
-<img src="https://static.igem.org/mediawiki/2014/1/19/OxigemDotP%26P.png" style="float:left;position:fixed; top:13.5%; height:4.375%;" />
-<img src="https://static.igem.org/mediawiki/2014/c/cc/OxigemDotTeam.png" style="float:left;position:fixed; top:3%; height:4.375%;" />
-<img id="modelling1" src="https://static.igem.org/mediawiki/2014/9/93/OxigemDotModelling1.png" style="display:none;float:left;position:fixed; top:59.3%; height:4.125%;" />
-<img id="achievements1" src="https://static.igem.org/mediawiki/2014/0/0f/OxigemDotAchievements1.png" style="display:none;float:left;position:fixed; top:71%; height:4%;" />
-<img id="igemcomm1" src="https://static.igem.org/mediawiki/2014/a/a8/OxigemDotiGEMcomm1.png" style="display:none;float:left;position:fixed; top:81.5%; height:4.375%;" />
-<img id="safety1" src="https://static.igem.org/mediawiki/2014/e/ee/OxigemDotSafety1.png" style="display:none;float:left;position:fixed; top:93%; height:4.125%;" />
-<img id="dcmation1" src="https://static.igem.org/mediawiki/2014/d/db/OxigemDotDCMation1.png" style="display:none;float:left;position:fixed; top:37%; height:4.125%;" />
-<img id="interlab1" src="https://static.igem.org/mediawiki/2014/5/52/OxigemDotInterlab1.png" style="display:none;float:left;position:fixed; top:25%; height:4.125%;" />
-<img id="policy1" src="https://static.igem.org/mediawiki/2014/b/bf/OxigemDotP%26P1.png" style="display:none;float:left;position:fixed; top:13.5%; height:4.375%;" />
-<img id="team1" src="https://static.igem.org/mediawiki/2014/c/c5/OxigemDotTeam1.png" style="display:none;float:left;position:fixed; top:3%; height:4.375%;" />
-<a href="#"><img class="heading" id="modelling" src="https://static.igem.org/mediawiki/2014/e/e0/OxigemSidebarModelling.png" style="opacity:0.8;float:left;position:fixed; top:59%; height:4.5%;"  /></a>
-<a href="#"><img class="heading" id="achievements" src="https://static.igem.org/mediawiki/2014/4/4a/OxigemSidebarAchievements.png" style="opacity:0.75;float:left;position:fixed; top:71%; height:4%;" /></a>
-<a href="#"><img class="heading" id="igemcomm" src="https://static.igem.org/mediawiki/2014/8/83/OxigemSidebariGEMcomm.png" style="opacity:0.8;float:left;position:fixed; top:81.1%; height:5.375%;" /></a>
-<a href="https://2014.igem.org/Team:Oxford/safety"><img class="heading" id="safety" src="https://static.igem.org/mediawiki/2014/3/3d/OxigemSidebarSafety.png" style="opacity:0.75;float:left;position:fixed; top:92.9%; height:4.375%;" /></a>
-<a href="#"><img class="heading" id="dcmation" src="https://static.igem.org/mediawiki/2014/1/18/OxigemSidebarDCMation.png" style="opacity:0.8;float:left;position:fixed; top:36%; height:5.75%;" /></a>
-<a href="#"><img class="heading" id="interlab" src="https://static.igem.org/mediawiki/2014/e/e2/OxigemSidebarInterlab.png" style="opacity:0.8;float:left;position:fixed; top:24.4%; height:5.25%;" /></a>
-<a href="https://2014.igem.org/Team:Oxford/policy_and_practices"><img class="heading" id="policy" src="https://static.igem.org/mediawiki/2014/7/7b/OxigemSidebarP%26P.png" style="opacity:0.8;float:left;position:fixed; top:13.2%; height:4.875%;" /></a>
-<a href="https://2014.igem.org/Team:Oxford/team"><img class="heading" id="team" src="https://static.igem.org/mediawiki/2014/3/3b/OxigemSidebarTeam.png" style="opacity:0.8;float:left;position:fixed; top:3%; height:4.625%;" /></a>
-<img src="https://static.igem.org/mediawiki/2014/6/60/OxigemAchievements2.png" style="position:fixed; display:none; height:4%; top:37%; left:2%;" />
-   <div class="iGEMlogo" style="width:6.5%; position:absolute; top:0.7%; right:0.5%; min-width:50px;">
-    <a href="https://2014.igem.org/Main_Page" target="_blank"><img src="https://static.igem.org/mediawiki/2014/5/56/OxigemiGEMgrey.png" style="width:100%"/></a>
-   </div>
-   <a href="#"><img id="arrowl" src="https://static.igem.org/mediawiki/2014/1/1d/OxigemArrowleft.png" style="position:fixed; width:50px; top:23%;right:0px; opacity:0.6; z-index:4;" /></a>
-   <div id="grey" style="width:190px; position:fixed; top:23%; right:-175px; z-index:4;">
-    <img src="https://static.igem.org/mediawiki/2014/0/0d/OxigemGrey.png" style="position:relative;width:100%;" />
-    <a href="#"><img id="arrowr" src="https://static.igem.org/mediawiki/2014/0/03/OxigemArrowr.png" style="position:absolute;width:14%;top:5%;left:10%;"></a>
-    <div class="fbicon" style="position:absolute;width:23%; top:20%; left:9%;" onmouseover=
-      "iconleft(this)" onmouseout="iconnormal(this)" border="0"><a href="https://www.facebook.com/oxfordigem" target="_blank" style="background-image: none;"><img src="https://static.igem.org/mediawiki/2014/8/88/OxigemIconfacebook.png" style="width:100%;" /></a>
-    </div>
-   <div class="twicon" style="position:absolute;width:23%; top:35%; left:9%;" onmouseover=
-      "iconleft(this)" onmouseout="iconnormal(this)" border="0">
-    <a href="https://twitter.com/OxfordiGEM" target="_blank" style="background-image: none;"><img src="https://static.igem.org/mediawiki/2014/3/3d/OxigemIgemtwitter.png" style="width:100%;" /></a>
-   </div>
-   <div class="yticon" style="position:absolute;width:23%; top:50%; left:9%;" onmouseover=
-      "iconleft(this)" onmouseout="iconnormal(this)" border="0">
-    <a href="https://www.youtube.com/channel/UCx1QJHqQcZ09aT97V2f4Xdw" target="_blank" style="background-image: none;"><img src="https://static.igem.org/mediawiki/2014/e/ea/OxigemIconyoutube.png" style="width:100%;" /></a>
-   </div>
-   <div class="oxicon" style="position:absolute;width:23%; top:65%; left:9%;" onmouseover=
-      "iconleft(this)" onmouseout="iconnormal(this)" border="0">
-    <a href="http://www.ox.ac.uk" target="_blank"><img src="https://static.igem.org/mediawiki/2014/8/8d/Iconoxford.png" style="width:100%;" /></a>
-   </div>
-   <div class="mailicon" style="position:absolute;width:23%; top:80%; left:9%;" onmouseover=
-      "iconleft(this)" onmouseout="iconnormal(this)" border="0" >
-    <a href="mailto:oxfordigem@bioch.ox.ac.uk" target="_blank" style="background-image: none;"><img src="https://static.igem.org/mediawiki/2014/3/35/OxigemIconmail.png" style="width:100%;" /></a>
-   </div>
 </body>
 </html>
+{{Team:Oxford/templates/footer}}

Team:Oxford/Modelling

From 2014.igem.org

Latest revision as of 03:44, 18 October 2014