Team:IIT Delhi/Modeling

From 2014.igem.org

(Difference between revisions)
 
(57 intermediate revisions not shown)
Line 6: Line 6:
{{CSS/Generic}}
{{CSS/Generic}}
{{CSS/js-image-slider}}
{{CSS/js-image-slider}}
 +
{{CSS/style2}}
 +
{{CSS/modeling}}
 +
<html>
<html>
<head>
<head>
-
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
     <meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1">
     <meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1">
     <meta name="description" content="iGEM 2014 IIT Delhi">
     <meta name="description" content="iGEM 2014 IIT Delhi">
-
     <meta name="keywords" content="igem iitdelhi 2014, biotech, biobricks, parts, notebook,  bio, chem, iit, delhi, hauz khas , new delhi, molecular biology,  genetics, synthetic, biology, competition, iGEM, MIT, USA">
+
     <meta name="keywords" content="igem iitdelhi 2014, biotech, biobricks, parts, notebook,  bio, chem, iit, delhi, hauz khas , new delhi, molecular biology,  genetics, synthetic, biology, competition, iGEM, MIT, USA, abhishek, bharti">
     <meta name="viewport" content="width=device-width, initial-scale=1">
     <meta name="viewport" content="width=device-width, initial-scale=1">
     <meta http-equiv="cache-control" content="public" />     
     <meta http-equiv="cache-control" content="public" />     
-
<title>iGEM IIT Delhi</title>
+
<title>iGEM IIT Delhi 2014</title>
-
<link rel='shortcut icon' href='/favicon.ico' />
+
<link rel='shortcut icon' id='favicon' href='https://static.igem.org/mediawiki/2014/7/76/Favicon3.png' />
  <link href='http://fonts.googleapis.com/css?family=Open+Sans' rel='stylesheet' type='text/css'>
  <link href='http://fonts.googleapis.com/css?family=Open+Sans' rel='stylesheet' type='text/css'>
<link href='http://fonts.googleapis.com/css?family=Droid+Serif:400italic' rel='stylesheet' type='text/css'>
<link href='http://fonts.googleapis.com/css?family=Droid+Serif:400italic' rel='stylesheet' type='text/css'>
<link href='http://fonts.googleapis.com/css?family=Roboto+Condensed:400,300,700' rel='stylesheet' type='text/css'>
<link href='http://fonts.googleapis.com/css?family=Roboto+Condensed:400,300,700' rel='stylesheet' type='text/css'>
 +
 +
 +
 +
 +
<link href='http://fonts.googleapis.com/css?family=Open+Sans:300,400,700' rel='stylesheet' type='text/css'>
 +
<!--map=====================-->
 +
<!--Script for google map at footer-->
 +
<!--
 +
<script
 +
src="http://maps.googleapis.com/maps/api/js?key=AIzaSyDY0kkJiTPVd2U7aTOAwhc9ySH6oHxOIYM&sensor=false">
 +
</script>
 +
 +
<script>
 +
function initialize()
 +
{
 +
var mapProp = {
 +
  center:new google.maps.LatLng(28.5450,77.1922),
 +
  zoom:5,
 +
  mapTypeId:google.maps.MapTypeId.ROADMAP
 +
  };
 +
var map=new google.maps.Map(document.getElementById("googleMap"),mapProp);
 +
}
 +
 +
google.maps.event.addDomListener(window, 'load', initialize);
 +
</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>
 +
 +
 +
 +
==============map ends-->
 +
 +
 +
 +
 +
<script src="http://ie7-js.googlecode.com/svn/version/2.1(beta4)/IE9.js"></script>
<script src="http://ie7-js.googlecode.com/svn/version/2.1(beta4)/IE9.js"></script>
Line 31: Line 86:
     });
     });
</script>
</script>
 +
</head>
</head>
 +
<body>
<body>
-
<div id="main-nav" >
 
-
  <nav class="top-bar" >
+
 
-
  <ul class="title-area">
+
<div id = "myDiv" style="display:none"><img id = "myImage" src = "images/https://static.igem.org/mediawiki/2014/e/ee/Namaste.gif"></div><br>
-
      <li class="name">
+
 
-
     
+
 
-
      <a href="https://2014.igem.org/Team:IIT_Delhi">  
+
 
-
      <span class="logo"><img src="https://static.igem.org/mediawiki/2014/e/e8/Iitdelhi_Logo.png" alt="logo" /></span></a>
+
 
-
      </li>
+
<div class="container_modeling">
-
     
+
<!--Header============================================-->
-
    </ul>
+
<div class="topblack"></div>
-
   
+
 
-
    <section class="top-bar-section">
+
<div class="topwhite">
-
     
+
<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>
-
      <!-- Left Nav Section -->
+
<div class="logotext"><img src="https://static.igem.org/mediawiki/2014/7/71/Text_iitd.jpg"/></div>
-
      <div id="main-menu" >
+
<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>
-
      <ul class="left nav">
+
 
-
        <li ><a href="https://2014.igem.org/Team:IIT_Delhi" >Home</a></li>
+
 
-
        <li><a href="https://2014.igem.org/Team:IIT_Delhi/Project" >Project</a>
+
<!-- Navigation bar======================================-->
-
              <ul>
+
  <div id="nav">
-
                <li ><a href="">Idea</a></li>
+
      <div id="nav_wrapper">
-
                <li><a href="">Need</a></li>  
+
        <ul>  
-
                <li ><a href="">Benefits</a></li>
+
            <li class="home"><a href="https://2014.igem.org/Team:IIT_Delhi">Home</a></li><li class="project">
-
                </ul>
+
            <a href="https://2014.igem.org/Team:IIT_Delhi/Project">Project</a></li><li class="nav_item_modeling" class="modeling">
-
                </li>
+
             <a href="https://2014.igem.org/Team:IIT_Delhi/Modeling">Modeling</a></li><li class="team">
-
        <li><a href="href="https://2014.igem.org/Team:IIT_Delhi/Parts" >Parts</a>
+
            <a href="https://2014.igem.org/Team:IIT_Delhi/Team">Team</a></li><li class="notebook">
-
              <ul>
+
            <a href="https://2014.igem.org/Team:IIT_Delhi/Notebook">Notebook</a></li><li class="attributions">
-
                <li ><a href="https://2014.igem.org/Team:IIT_Delhi/Parts">Biobricks Submitted</a></li>
+
            <a href="https://2014.igem.org/Team:IIT_Delhi/Attributions">Attributions</a></li><li class="safety">
-
                <li><a href="">Previous Parts Improved</a></li>
+
            <a href="https://2014.igem.org/Team:IIT_Delhi/Safety">Safety</a></li><li class="parts">
-
                </ul>
+
            <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>
-
                </li>
+
      </ul>
-
             <li><a href="https://2014.igem.org/Team:IIT_Delhi/Modeling" >Modeling</a></li>
+
-
        <li><a href="" >Team</a>
+
-
                <ul>
+
-
                <li ><a href="https://2014.igem.org/Team:IIT_Delhi/Team">Team Roster</a></li>
+
-
                <li><a href="https://igem.org/Team.cgi?id=1395">Official Team  Profile</a></li>  
+
-
                </ul>
+
-
</li>
+
-
        <li><a href="https://2014.igem.org/Team:IIT_Delhi/Notebook" >Notebook</a></li>
+
-
            <li><a href="https://2014.igem.org/Team:IIT_Delhi/Safety" >Safety</a></li>
+
-
        <li><a href="https://2014.igem.org/Team:IIT_Delhi/Attributions" >Attributions</a></li>
+
-
        <li><a href="https://2014.igem.org/Team:IIT_Delhi/sponsors" >Sponsors</a></li>
+
-
      </ul>
+
       </div>
       </div>
-
      </section>
+
  </div>
-
      <!-- Right Nav Section -->
+
-
      <ul>
+
-
      <li> <a href="https://2014.igem.org/">
+
-
      <span class="igem-logo"><img src="https://static.igem.org/mediawiki/2014/f/ff/Iitd_Igemlogo_officiallogo_iitd.png" alt="logo" /></span></a>
+
-
     
 
-
      </li>
 
-
     
 
-
    </ul>
 
-
   
 
-
    </section>
 
-
  </nav>
 
-
</div>
 
-
<div>
+
<!--Follow us link===============-->
-
<ul >
+
<div class="links">
-
      <li>
+
<p class="followus">Follow Us</p>
-
<a href="http://www.mahindra.com">  
+
      <div class="link_bg">
-
      <span class="mahindra" style="margin-top:40px;"><img src="https://static.igem.org/mediawiki/2014/3/3d/Mahindra-rise-web-logo.png" alt="mahindra" /></span></a>
+
            <table border="0" cellspacing="2">
 +
              <tr>
 +
                <td>
 +
                <a href="https://www.facebook.com/igemiitdelhi" target="_blank"><img src="https://static.igem.org/mediawiki/2014/5/51/Fb.png" alt="facebook" title="Facebook" onmouseover="this.src='https://static.igem.org/mediawiki/2014/6/6c/Fbhover.png';"
 +
            onmouseout="this.src='https://static.igem.org/mediawiki/2014/5/51/Fb.png';" /> </a>              </td>
 +
             
 +
                <td >
 +
                <a href="https://twitter.com/iGEM_IIT_Delhi" target="_blank" >
 +
                <img src="https://static.igem.org/mediawiki/2014/f/f7/Twitter.png" alt="twitter" title="Twitter" onmouseover="this.src='https://static.igem.org/mediawiki/2014/5/56/Twitterhover.png';"
 +
            onmouseout="this.src='https://static.igem.org/mediawiki/2014/f/f7/Twitter.png';"/></a>               </td>
 +
             
 +
                <td>
 +
                <a href="https://www.youtube.com/channel/UCBHF9Lel4MF2dien-p3o10A" target="_blank" >
 +
                <img src="https://static.igem.org/mediawiki/2014/a/af/Youtube.png" alt="you tube" title="Youtube" onmouseover="this.src='https://static.igem.org/mediawiki/2014/9/91/Youtubehover.png';"
 +
            onmouseout="this.src='https://static.igem.org/mediawiki/2014/a/af/Youtube.png';"/></a>                </td>
 +
              </tr>
 +
             
 +
            </table>
 +
        </div>
 +
 
-
     
 
-
      </li>
 
-
     
 
-
    </ul>
 
</div>
</div>
-
 
 
-
    <!--CONTENT OF HEADER STARTS-->
 
-
    <header class="center">
 
-
           
+
</div><!--Topwhite ends========-->
-
    </header>
+
<!-- Main Content Starts-->
-
    <!--CONTENT OF HEADER ENDSSS-->
+
-
               
+
<div class="topimg">
-
<div style="clear:both"></div>
+
     <img src="https://static.igem.org/mediawiki/2014/2/22/Igem-iitd-modeling.jpg"/>
-
     <!--CONTENT FOR DESIGN RESERVED SIZE="1000px X 200px" STARTS-->
+
</div>
-
   
+
-
    <!--CONTENT FOR DESIGN RESERVED SIZE="1000px X 200px" STARTS-->
+
-
    <div style="clear:both"></div>
+
-
    <!--MAIN HOVER EFFECT STARTS FROM HERE-->
+
<div class="layout">
-
   
+
-
    <!--MAIN HOVER EFFECT ENDSS FROM HERE -->
+
-
+
-
  <!--CONTENT OF FOOTER-STRIP STARTS-->
+
-
   
+
-
    <!--CONTENT OF FOOTER-STRIP ENDS-->
+
 +
<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>
-
</div>
+
</ul>
-
<!--main content -->
+
<br>
-
<table width="70%" align="center">
+
<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>
-
<!--welcome box -->
+
<center>The curve of mRNA concentration versus time</center>
-
<tr>
+
<div class="vector"><img src="https://static.igem.org/mediawiki/2014/6/6e/Igem-iitd-modeling-4.jpg"/></div>
-
<td style="border:1px solid black;" colspan="3" align="center" height="150px" bgColor=#FF404B>
+
<br><div class="vector"><img src="https://static.igem.org/mediawiki/2014/4/4b/Igem-iitd-modeling-5.jpg"/></div>
-
<h1 >WELCOME TO iGEM 2014! </h1>
+
<br>
-
<p>Your team has been approved and you are ready to start the iGEM season!
+
<center>Conclusions</center>
-
<br>On this page you can document your project, introduce your team members, document your progress <br> and share your iGEM experience with the rest of the world! </p>
+
<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>
<br>
-
<p style="color:#E7E7E7"> <a href="https://2014.igem.org/wiki/index.php?title=Team:IIT_Delhi/Modeling&action=edit"style="color:#FFFFFF"> Click here  to edit this page!</a> </p>
 
-
</td>
 
-
</tr>
 
-
<!-- end welcome box -->
+
<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>
-
<!--navigation menu -->
 
-
<!--modeling content -->
 
-
<tr><td colspan="3"> <h3>Modeling</h3></td></tr>
 
-
</tr>
 
-
<tr>
 
-
<td width="45%"  valign="top">
 
-
<p>If you choose to create a model during your project, please write about it here. Modeling is not an essential part of iGEM, but we encourage any and all teams to model some aspect of their project. See previous "Best Model" awards for more information.</p>
 
-
</td>
 
-
<td></td>
 
-
<td></td>
 
-
</tr>
 
-
</table>
+
 
-
<div id="headerstrip_bottom" style="margin-left:120px; alignment-baseline:hanging;" >
+
 
-
  <nav id="navigation_bottom" >
+
 
-
        <table class="hello" >
+
 
-
          <tr>
+
 
-
            <td><a href="" title="About us" style="margin-right:42px;">About us</a></td>
+
 
-
            <td><a href="" title="Privacy policy" style="margin-right:42px;padding-bottom:6px;">Safety</a></td>
+
 
-
            <td><a href="" title="Hospitality" style="margin-right:42px;padding-bottom:6px;">Attributions</a></td>
+
 
-
            <td><a href="" title="Contact us" style="margin-right:42px;padding-bottom:6px;">Contact us</a></td>  
+
 
-
            <td><a href="" title="Gallery" style="padding-bottom:6px;">Gallery</a></td>
+
 
-
          </tr>
+
 
-
        </table>
+
 
-
      </nav>
+
</div>
-
</div>
+
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
<div class="footerbg_modeling">
 +
 
 +
<div class="nav2">
 +
<table class="nav2table">
 +
  <tr>
 +
    <td><a href="https://2014.igem.org/Team:IIT_Delhi">HOME</a></td><td>|</td>
 +
    <td><a href="https://2014.igem.org/Team:IIT_Delhi/Project">PROJECT</a></td><td>|</td>
 +
    <td><a href="https://2014.igem.org/Team:IIT_Delhi/Modeling">MODELING</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/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/Parts">PARTS</a></td><td>|</td>
 +
    <td><a href="https://2014.igem.org/Team:IIT_Delhi/Achievements">ACHIEVEMENTS</a></td>
 +
  </tr>
 +
</table>
 +
</div>
 +
<div class="copyright"><p>Copyright &copy; iGEM-IIT Delhi 2014 | Developer: ABHISHEK BHARTI & SHASHANK YADAV </p>
 +
<center>"We won a Bronze Medal at the iGEM Giant Jamboree 2014"</center></div>
 +
 
 +
</div>
 +
 
 +
</div>
 +
</body>
</body>
</html>
</html>

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"