Team:Manchester/Modellingtest

From 2013.igem.org

(Difference between revisions)
 
(57 intermediate revisions not shown)
Line 1: Line 1:
{{:Team:Manchester/layout/noheader}}
{{:Team:Manchester/layout/noheader}}
-
{{:Team:Manchester/Navbartest}}
+
{{:Team:Manchester/Navbartest3}}
{{:Team:Manchester/Footer}}
{{:Team:Manchester/Footer}}
Line 73: Line 73:
position:relative;
position:relative;
width:950px;
width:950px;
-
height:2500px;
+
height:900px;
}
}
 +
 +
.mtextbox {
 +
    width: 100%;
 +
    min-height: 80px;
 +
    height: auto;
 +
    background-color: white;
 +
    color: #4c0082;
 +
    font-face: Trebuchet Sans MS;
 +
    font-size: 20px;
 +
    margin: 10px 0;
 +
    text-align: center;
 +
  }
 +
  .mtextbox b {
 +
    color: #660099;
 +
  }
.wrapper
.wrapper
Line 81: Line 96:
clear:both;
clear:both;
width:951px;
width:951px;
-
top:110px;
+
top:120px;
left:0;
left:0;
background-color:white;
background-color:white;
-
padding-left:8px;
+
padding:10px;
-webkit-box-shadow: 0px 0px 5px 0px rgba(0,0,0,0.75);
-webkit-box-shadow: 0px 0px 5px 0px rgba(0,0,0,0.75);
Line 92: Line 107:
/******************************************************containers*****************************************************/
/******************************************************containers*****************************************************/
-
.column1, .column2, .column3
+
.column1
{
{
  float:left;
  float:left;
  width:300px;
  width:300px;
-
  height:555px;
+
  height:520px;
-
  margin:7px;
+
  margin:8px;
  padding:0;
  padding:0;
-
  background-color:#E6E6E6;
+
  background-color:#CCC;
   
   
  -webkit-box-shadow: 0px 0px 5px 0px rgba(0,0,0,0.75);
  -webkit-box-shadow: 0px 0px 5px 0px rgba(0,0,0,0.75);
Line 107: Line 122:
}
}
-
.column1 img, .column2 img, .column3 img
+
.column1 .left
{
{
-
margin:5px 0 5px 60px;
+
float:left;
 +
  margin:10px 0 10px 10px;
   -webkit-box-shadow: 0px 0px 5px 0px rgba(0,0,0,0.75);
   -webkit-box-shadow: 0px 0px 5px 0px rgba(0,0,0,0.75);
Line 116: Line 132:
}
}
 +
.column1 .right
 +
{
 +
float:right;
 +
margin:10px 10px 10px 0;
 +
  -webkit-box-shadow: 0px 0px 5px 0px rgba(0,0,0,0.75);
 +
-moz-box-shadow: 0px 0px 5px 0px rgba(0,0,0,0.75);
 +
box-shadow: 0px 0px 5px 0px rgba(0,0,0,0.75);
 +
}
-
/******************************************************next button*****************************************************/
+
.column1 p
-
.next a
+
{
{
-
width:185px;
+
clear:both;
-
text-decoration:none;
+
margin:0 auto;
-
color:white;
+
display:block;
-
position:fixed;
+
width:260px;
-
bottom:5px;
+
height:265px;
-
right:5px;
+
font-style:Trebuchest MS;
-
text-align:center;
+
font-size:14px;
-
background:#606060;
+
color:#4C0082;
-
padding:15px;
+
padding:10px;
-
font-style:Trebuchet MS;
+
background:#F2F2F2;
-
font-weight:bold;
+
text-align:justify;
-
font-size:26px;
+
 
-
color:white;
+
  -webkit-box-shadow: 0px 0px 5px 0px rgba(0,0,0,0.75);
 +
-moz-box-shadow: 0px 0px 5px 0px rgba(0,0,0,0.75);
 +
box-shadow: 0px 0px 5px 0px rgba(0,0,0,0.75);
}
}
-
.next a:hover
+
.column2
{
{
-
background:#C0C0C0;
+
float:left;
-
color:#606060;
+
width:455px;
 +
margin:8px;
 +
padding:0;
 +
background-color:#CCC;
 +
 +
-webkit-box-shadow: 0px 0px 5px 0px rgba(0,0,0,0.75);
 +
-moz-box-shadow: 0px 0px 5px 0px rgba(0,0,0,0.75);
 +
box-shadow: 0px 0px 5px 0px rgba(0,0,0,0.75);
 +
}
}
-
/******************************************************back button*****************************************************/
+
.column2 .left
-
.back a
+
{
{
-
width:180px;
+
float:left;
-
text-decoration:none;
+
margin:10px 0 10px 10px;
-
color:white;
+
-
position:fixed;
+
-
bottom:5px;
+
-
left:5px;
+
-
text-align:center;
+
-
background:#606060;
+
-
padding:15px;
+
-
font-style:Trebuchet MS;
+
-
font-weight:bold;
+
-
font-size:26px;
+
-
color:white;
+
 +
  -webkit-box-shadow: 0px 0px 5px 0px rgba(0,0,0,0.75);
 +
-moz-box-shadow: 0px 0px 5px 0px rgba(0,0,0,0.75);
 +
box-shadow: 0px 0px 5px 0px rgba(0,0,0,0.75);
}
}
-
.back a:hover
+
.column2 .right
{
{
-
background:#C0C0C0;
+
float:left;
-
color:#606060;
+
margin:10px 10px 10px 15px;
 +
 
 +
  -webkit-box-shadow: 0px 0px 5px 0px rgba(0,0,0,0.75);
 +
-moz-box-shadow: 0px 0px 5px 0px rgba(0,0,0,0.75);
 +
box-shadow: 0px 0px 5px 0px rgba(0,0,0,0.75);
}
}
 +
.column2 p
 +
{
 +
clear:both;
 +
margin:10px;
 +
display:block;
 +
width:415px;
 +
font-style:Trebuchest MS;
 +
font-size:14px;
 +
color:#4C0082;
 +
padding:10px;
 +
background:#F2F2F2;
 +
text-align:justify;
 +
 +
  -webkit-box-shadow: 0px 0px 5px 0px rgba(0,0,0,0.75);
 +
-moz-box-shadow: 0px 0px 5px 0px rgba(0,0,0,0.75);
 +
box-shadow: 0px 0px 5px 0px rgba(0,0,0,0.75);
 +
}
</style>
</style>
Line 177: Line 222:
<div class="banner">
<div class="banner">
  <div class="igem">  
  <div class="igem">  
-
  <a>
+
  <a href="https://2013.igem.org/Main_Page">
           <img src="https://static.igem.org/mediawiki/2013/3/3f/Igem.png">
           <img src="https://static.igem.org/mediawiki/2013/3/3f/Igem.png">
           </a>
           </a>
Line 196: Line 241:
</div>  
</div>  
</div>
</div>
 +
 +
 +
 +
 +
 +
<div class="global">
<div class="global">
<div class="wrapper" >
<div class="wrapper" >
-
                <div class="column1">
+
<div class="mtextbox">
-
    <img src="https://static.igem.org/mediawiki/2013/e/ea/Ethics.jpg" width="180" height="210" />
+
  <center><b><u>Key Achievements</b></u><br></center>
-
                       
+
<center>• Produced iGEM's first ever model based on uncertainty analysis</center>
 +
<center>• Used modelling to directly influence experimental and human practices work</center>
 +
<center>• Utilised two different types of uncertainty modelling</center>
 +
<center>• Collaborated with other UK iGEM teams</center>
 +
</div>
 +
    <div class="column2">
 +
      <a href="https://2013.igem.org/Team:Manchester/parametertest"><img src="https://static.igem.org/mediawiki/2013/4/4e/Enzymesensitivities.png" width="120" height="210" class="left"/></a>
 +
      <img src="https://static.igem.org/mediawiki/2013/2/22/Colourfulmodelmodelmodel.png" width="300" height="210" class="right"/>
 +
                <p> Enzymes in the FAB pathway showed a lack of experimentally determined kinetic parameters. To account for this, we used probability distributions for each individual parameter defined with respect to the uncertainty of the value. We were then able to generate not one but a <i>series</i> of unbiased models to illustrate the FAB pathway. We believe that this innovative approach to modelling appropriately addresses uncertainties in biology and is important for use in future computational investigations.
 +
      </p>       
</div>
</div>
-
<div class="column1">
+
             
-
         <img src="https://static.igem.org/mediawiki/2013/9/9f/Projectpartspageresized.jpg" width="180" height="210"/>                    
+
<div class="column2">
 +
         <a href="https://2013.igem.org/Team:Manchester/fabAmodeltest"><img src="https://static.igem.org/mediawiki/2013/4/46/FabAman.png" width="120" height="210" class="left"/></a>
 +
        <img src="https://static.igem.org/mediawiki/2013/4/48/FabA_cartoon_mesh.png" width="300" height="210" class="right"/>   
 +
                <p>Trying to experimentally study the overexpression of some enzymes critically involved in palm oil synthesis, as predicted by our “system” level model isn’t easy, particularly when they are involved in cyclic reactions (eg FAB pathway). Our strategy was to simply add a His-tag to the N- and C-terminus of βHACdH, but to make it even more complex βHACdH is a homodimer. Therefore, we did another model but this time of the molecular dynamics kind to see which terminal, if any, would be best to add the His-tags to.
 +
</p>       
</div>
</div>
-
+
           
-
<div class="column1">
+
<div class="column2">
-
    <img src="https://static.igem.org/mediawiki/2013/7/7e/Aimresized.jpg" width="180" height="210" />
+
      <a href="https://2013.igem.org/Team:Manchester/popdynamictest"><img src="https://static.igem.org/mediawiki/2013/8/84/DynamicMan.png" width="120" height="210" class="left"/></a>
-
                       
+
      <img src="https://static.igem.org/mediawiki/2013/9/9a/Popdynm.png" width="300" height="210" class="right"/>
 +
                <p> As part of our Human Practices investigations, we created a series of in depth population dynamics models to show the impact that the palm oil industry has on the population of the  Sumatran Orangutan. We were then able to project this into the future to demonstrate a series of likely scenarios. Sadly, things are looking pretty bleak for the Orangutan - however, it appears there could be a way to save them...
 +
      </p>       
 +
</div>
 +
           
 +
<div class="column2">
 +
      <a href="https://2013.igem.org/Team:Manchester/collabtest"><img src="https://static.igem.org/mediawiki/2013/b/b1/ModellingMan1.png" width="120" height="210" class="left"/></a>
 +
      <img src="https://static.igem.org/mediawiki/2013/e/e2/Collaboraboraboraboraboraboration.jpg" width="300" height="210" class="right"/>
 +
                <p> Here at Manchester iGEM team, we believe that modelling is a vital step in the production of any synthetic biology system. However, often the production of such models can be hindered or left out altogether due to lack of expertise and outside help. With this in mind, we enlisted the help of another two UK iGEM teams in a quest to educate the iGEM community about the software available to them.      </p>       
</div>
</div>
</div>
</div>
-
      <div class="next">
 
-
        <a href="https://2013.igem.org/Team:Manchester/Projecttest" class="nextButton">Next</a>
 
-
      </div>
 
-
 
-
      <div class="back">
 
-
        <a href="https://2013.igem.org/Team:Manchester/Hometest" class="backButton">Previous</a>
 
-
      </div>
 
-
 
</div>
</div>
</body>
</body>
</html>
</html>

Latest revision as of 18:32, 26 October 2013

page

Top

Safety

Key Achievements
• Produced iGEM's first ever model based on uncertainty analysis
• Used modelling to directly influence experimental and human practices work
• Utilised two different types of uncertainty modelling
• Collaborated with other UK iGEM teams

Enzymes in the FAB pathway showed a lack of experimentally determined kinetic parameters. To account for this, we used probability distributions for each individual parameter defined with respect to the uncertainty of the value. We were then able to generate not one but a series of unbiased models to illustrate the FAB pathway. We believe that this innovative approach to modelling appropriately addresses uncertainties in biology and is important for use in future computational investigations.

Trying to experimentally study the overexpression of some enzymes critically involved in palm oil synthesis, as predicted by our “system” level model isn’t easy, particularly when they are involved in cyclic reactions (eg FAB pathway). Our strategy was to simply add a His-tag to the N- and C-terminus of βHACdH, but to make it even more complex βHACdH is a homodimer. Therefore, we did another model but this time of the molecular dynamics kind to see which terminal, if any, would be best to add the His-tags to.

As part of our Human Practices investigations, we created a series of in depth population dynamics models to show the impact that the palm oil industry has on the population of the Sumatran Orangutan. We were then able to project this into the future to demonstrate a series of likely scenarios. Sadly, things are looking pretty bleak for the Orangutan - however, it appears there could be a way to save them...

Here at Manchester iGEM team, we believe that modelling is a vital step in the production of any synthetic biology system. However, often the production of such models can be hindered or left out altogether due to lack of expertise and outside help. With this in mind, we enlisted the help of another two UK iGEM teams in a quest to educate the iGEM community about the software available to them.

Retrieved from "http://2013.igem.org/Team:Manchester/Modellingtest"