Team:IIT Delhi/Modeling

From 2014.igem.org

(Difference between revisions)
 
(39 intermediate revisions not shown)
Line 29: Line 29:
<link href='http://fonts.googleapis.com/css?family=Open+Sans:300,400,700' rel='stylesheet' type='text/css'>
<link href='http://fonts.googleapis.com/css?family=Open+Sans:300,400,700' rel='stylesheet' type='text/css'>
-
<!--map=====================
+
<!--map=====================-->
<!--Script for google map at footer-->
<!--Script for google map at footer-->
 +
<!--
<script
<script
src="http://maps.googleapis.com/maps/api/js?key=AIzaSyDY0kkJiTPVd2U7aTOAwhc9ySH6oHxOIYM&sensor=false">
src="http://maps.googleapis.com/maps/api/js?key=AIzaSyDY0kkJiTPVd2U7aTOAwhc9ySH6oHxOIYM&sensor=false">
Line 48: Line 49:
google.maps.event.addDomListener(window, 'load', initialize);
google.maps.event.addDomListener(window, 'load', initialize);
</script>
</script>
 +
<script type="text/javascript">
 +
 +
  (function(){
 +
    var myDiv = document.getElementById("myDiv");
 +
 +
    var show = function(){
 +
      myDiv.style.display = "block";
 +
      setTimeout(hide, 5000);  // 5 seconds
 +
    }
 +
 +
    var hide = function(){
 +
      myDiv.style.display = "none";
 +
    }
 +
 +
    show();
 +
  })();
 +
 +
</script>
 +
Line 73: Line 93:
-
<div class="container">
+
<div id = "myDiv" style="display:none"><img id = "myImage" src = "images/https://static.igem.org/mediawiki/2014/e/ee/Namaste.gif"></div><br>
 +
 
 +
 
 +
 
 +
 
 +
<div class="container_modeling">
<!--Header============================================-->
<!--Header============================================-->
<div class="topblack"></div>
<div class="topblack"></div>
<div class="topwhite">
<div class="topwhite">
-
<div class="logo"><a href="https://2014.igem.org/Team:IIT_Delhi"><img src="https://static.igem.org/mediawiki/2014/0/08/Iitdigemlogo.png"/></a></div>
+
<div class="logo"><a href="https://2014.igem.org/Team:IIT_Delhi"><img src="https://static.igem.org/mediawiki/2014/b/b4/Logo_igem_iitdelhi.png"/></a></div>
 +
<div class="logotext"><img src="https://static.igem.org/mediawiki/2014/7/71/Text_iitd.jpg"/></div>
<div class="igemlogo"><a href="https://igem.org/Main_Page" target="_blank"><img src="https://static.igem.org/mediawiki/2014/e/e2/Igemlogo.png"/></a></div>
<div class="igemlogo"><a href="https://igem.org/Main_Page" target="_blank"><img src="https://static.igem.org/mediawiki/2014/e/e2/Igemlogo.png"/></a></div>
Line 85: Line 111:
   <div id="nav">
   <div id="nav">
       <div id="nav_wrapper">
       <div id="nav_wrapper">
-
         <ul>
+
         <ul>  
             <li class="home"><a href="https://2014.igem.org/Team:IIT_Delhi">Home</a></li><li class="project">
             <li class="home"><a href="https://2014.igem.org/Team:IIT_Delhi">Home</a></li><li class="project">
             <a href="https://2014.igem.org/Team:IIT_Delhi/Project">Project</a></li><li class="nav_item_modeling" class="modeling">
             <a href="https://2014.igem.org/Team:IIT_Delhi/Project">Project</a></li><li class="nav_item_modeling" class="modeling">
             <a href="https://2014.igem.org/Team:IIT_Delhi/Modeling">Modeling</a></li><li class="team">
             <a href="https://2014.igem.org/Team:IIT_Delhi/Modeling">Modeling</a></li><li class="team">
             <a href="https://2014.igem.org/Team:IIT_Delhi/Team">Team</a></li><li class="notebook">
             <a href="https://2014.igem.org/Team:IIT_Delhi/Team">Team</a></li><li class="notebook">
-
             <a href="https://2014.igem.org/Team:IIT_Delhi/Notebook">Notebook</a></li><li class="attribute">
+
             <a href="https://2014.igem.org/Team:IIT_Delhi/Notebook">Notebook</a></li><li class="attributions">
-
             <a href="https://2014.igem.org/Team:IIT_Delhi/Attributions">Attribute</a></li><li class="safety">
+
             <a href="https://2014.igem.org/Team:IIT_Delhi/Attributions">Attributions</a></li><li class="safety">
             <a href="https://2014.igem.org/Team:IIT_Delhi/Safety">Safety</a></li><li class="parts">
             <a href="https://2014.igem.org/Team:IIT_Delhi/Safety">Safety</a></li><li class="parts">
-
             <a href="https://2014.igem.org/Team:IIT_Delhi/Parts">Parts</a></li>
+
             <a href="https://2014.igem.org/Team:IIT_Delhi/Parts">Parts</a></li><li class="achievements"><a href="https://2014.igem.org/Team:IIT_Delhi/Achievements">Achievements</a></li>
       </ul>
       </ul>
       </div>
       </div>
Line 127: Line 153:
-
<div style="margin-top:200px">
 
-
    <a href="https://www.gmail.com">Case Study Competition</a></div>
 
</div><!--Topwhite ends========-->
</div><!--Topwhite ends========-->
 +
<!-- Main Content Starts-->
 +
<div class="topimg">
 +
    <img src="https://static.igem.org/mediawiki/2014/2/22/Igem-iitd-modeling.jpg"/>
 +
</div>
 +
<div class="layout">
 +
<center>Synthetic Biology targets to design and create original biological systems. But the genetic systems involved are very intricate. Before going to lab and start working,  one should first have a reasonable estimate of what they expect to do. And here mathematical modeling is useful.</center>
 +
<br>
 +
<center>Mathematical Model</center>
 +
<ul>The following assumptions were taken for modeling the system:
 +
    <li> &#10004; All the cells behaves the same way in our system</li>
 +
    <li> &#10004;Our consideration of the concentrations of mRNA and Protein starts from t=0, and there concentration is zero at t=0</li>
 +
    <li> &#10004; We have assumed the mRNA concentration to be "x" and protein concentration to be "y"</li>
 +
</ul>
 +
<br>
 +
<ul>We chose a constitutive promoter so the input gene expression function do not involve any repression or activation term, So formulated the following set of differential equations of transcription and translation:
 +
   
 +
<br>
 +
<div class="vector"><img src="https://static.igem.org/mediawiki/2014/0/07/Igem-iitd-modeling-1.jpg"/></div>
 +
<br>The meaning of the respective symbols is given in the Parameter table below
 +
<br>
 +
We used some of the parameters developed by iGEM Team Aberdeen 2009 and for the maximal expression level of promoter J231119 we compared is RPU(Relative promoter unit) values with promoter J23101.
 +
<br>
 +
<center>Parameters</center>
 +
<div class="vector"><img src="https://static.igem.org/mediawiki/2014/0/05/Igem-iitd-modeling-2.jpg"/></div>
 +
<br>
 +
After putting values the set of differential equation becomes:
 +
<div class="vector"><img src="https://static.igem.org/mediawiki/2014/4/4d/Igem-iitd-modeling-3.jpg"/></div>
 +
<br>
 +
After solving these in MATLAB we get the following curves:
 +
<br>
 +
<center>The curve of mRNA concentration versus time</center>
 +
<div class="vector"><img src="https://static.igem.org/mediawiki/2014/6/6e/Igem-iitd-modeling-4.jpg"/></div>
 +
<br><div class="vector"><img src="https://static.igem.org/mediawiki/2014/4/4b/Igem-iitd-modeling-5.jpg"/></div>
 +
<br>
 +
<center>Conclusions</center>
 +
<li> &#10004; Our design works as expected showing the work of a constitutive promoter</li>
 +
<li> &#10004; Another important point is that by modeling our system, we are able to get an idea about the number of protein molecules present finally after 7200 s, the number is 12 x 10^4 , which is quite high compared to the total count of all proteins present in E Coli </li>
 +
<br>
 +
<ul>References:<br>
 +
<li>1 http://kirschner.med.harvard.edu/files/bionumbers/fundamentalBioNumbersHandout.pdf </li>
 +
<li>2 http://www.jbc.org/content/277/26/23664.full.pdf </li>
 +
<li>3 http://www.scielo.br/pdf/gmb/v27n3/a22v27n3.pdf </li>
 +
<li>4 http://deepblue.lib.umich.edu/bitstream/handle/2027.42/22607/0000157.pdf?sequence=1 </li>
 +
</ul>
Line 150: Line 218:
-
<!--Footer===========================================-->
 
-
<div class="footer">
+
 
-
<div class="flagview">
+
 
-
    <a href="http://info.flagcounter.com/AJ8u"><img src="http://s11.flagcounter.com/count/AJ8u/bg_373737/txt_FFFFFF/border_373737/columns_3/maxflags_10/viewers_0/labels_1/pageviews_1/flags_1/" alt="Free counters!" border="0">
+
 
-
    </a>
+
 
-
</div>
+
 
-
<!-- Navigation bar at footer-->
+
 
 +
 
 +
 
 +
</div>
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
<div class="footerbg_modeling">
 +
 
<div class="nav2">
<div class="nav2">
  <table class="nav2table">
  <table class="nav2table">
Line 166: Line 244:
     <td><a href="https://2014.igem.org/Team:IIT_Delhi/Team">TEAM</a></td><td>|</td>
     <td><a href="https://2014.igem.org/Team:IIT_Delhi/Team">TEAM</a></td><td>|</td>
     <td><a href="https://2014.igem.org/Team:IIT_Delhi/Notebook">NOTEBOOK</a></td><td>|</td>
     <td><a href="https://2014.igem.org/Team:IIT_Delhi/Notebook">NOTEBOOK</a></td><td>|</td>
-
     <td><a href="https://2014.igem.org/Team:IIT_Delhi/Attributes">ATTRIBUTES</a></td><td>|</td>
+
     <td><a href="https://2014.igem.org/Team:IIT_Delhi/Attributions">ATTRIBUTIONS</a></td><td>|</td>
     <td><a href="https://2014.igem.org/Team:IIT_Delhi/Safety">SAFETY</a></td><td>|</td>
     <td><a href="https://2014.igem.org/Team:IIT_Delhi/Safety">SAFETY</a></td><td>|</td>
-
     <td><a href="https://2014.igem.org/Team:IIT_Delhi/Parts">PARTS</a></td>
+
     <td><a href="https://2014.igem.org/Team:IIT_Delhi/Parts">PARTS</a></td><td>|</td>
 +
    <td><a href="https://2014.igem.org/Team:IIT_Delhi/Achievements">ACHIEVEMENTS</a></td>
   </tr>
   </tr>
  </table>
  </table>
</div>
</div>
-
<div class="maplink">
+
<div class="copyright"><p>Copyright &copy; iGEM-IIT Delhi 2014 | Developer: ABHISHEK BHARTI & SHASHANK YADAV </p>
-
  <table class="maptable">
+
<center>"We won a Bronze Medal at the iGEM Giant Jamboree 2014"</center></div>
-
    <tr><td><a href="http://www.iitd.ac.in/" target="_blank">Indian Institute of Technology (IIT) Delhi, India</a></td>
+
-
        <td>|</td>
+
-
        <td><a href="https://www.google.com/maps/place/Indian+Institute+of+Technology+Delhi" target="_blank">View Map</a></td><td></td>
+
-
    </tr>
+
-
  </table>
+
-
</div>
+
-
<div class="copyright"><p>Copyright &copy; iGEM-IIT Delhi 2014 </p></div>
+
-
 
+
</div>
</div>
-
 
-
 
-
 
</div>
</div>

Latest revision as of 10:48, 30 November 2014


iGEM IIT Delhi 2014


Follow Us

facebook twitter you tube
Synthetic Biology targets to design and create original biological systems. But the genetic systems involved are very intricate. Before going to lab and start working, one should first have a reasonable estimate of what they expect to do. And here mathematical modeling is useful.

Mathematical Model
    The following assumptions were taken for modeling the system:
  • ✔ All the cells behaves the same way in our system
  • ✔Our consideration of the concentrations of mRNA and Protein starts from t=0, and there concentration is zero at t=0
  • ✔ We have assumed the mRNA concentration to be "x" and protein concentration to be "y"

    We chose a constitutive promoter so the input gene expression function do not involve any repression or activation term, So formulated the following set of differential equations of transcription and translation:

    The meaning of the respective symbols is given in the Parameter table below
    We used some of the parameters developed by iGEM Team Aberdeen 2009 and for the maximal expression level of promoter J231119 we compared is RPU(Relative promoter unit) values with promoter J23101.
    Parameters

    After putting values the set of differential equation becomes:

    After solving these in MATLAB we get the following curves:
    The curve of mRNA concentration versus time


    Conclusions
  • ✔ Our design works as expected showing the work of a constitutive promoter
  • ✔ Another important point is that by modeling our system, we are able to get an idea about the number of protein molecules present finally after 7200 s, the number is 12 x 10^4 , which is quite high compared to the total count of all proteins present in E Coli

      • References:
    • 1 http://kirschner.med.harvard.edu/files/bionumbers/fundamentalBioNumbersHandout.pdf
    • 2 http://www.jbc.org/content/277/26/23664.full.pdf
    • 3 http://www.scielo.br/pdf/gmb/v27n3/a22v27n3.pdf
    • 4 http://deepblue.lib.umich.edu/bitstream/handle/2027.42/22607/0000157.pdf?sequence=1
HOME| PROJECT| MODELING| TEAM| NOTEBOOK| ATTRIBUTIONS| SAFETY| PARTS| ACHIEVEMENTS

Copyright © iGEM-IIT Delhi 2014 | Developer: ABHISHEK BHARTI & SHASHANK YADAV

"We won a Bronze Medal at the iGEM Giant Jamboree 2014"

Retrieved from "http://2014.igem.org/Team:IIT_Delhi/Modeling"