Team:Penn/Modeling

From 2013.igem.org

(Difference between revisions)
 
(18 intermediate revisions not shown)
Line 6: Line 6:
     <script src="https://googledrive.com/host/0B4ZBZOYYKBzEZTdBSFdUV19LYjQ" type="text/javascript"></script>
     <script src="https://googledrive.com/host/0B4ZBZOYYKBzEZTdBSFdUV19LYjQ" type="text/javascript"></script>
<script src="https://googledrive.com/host/0B4ZBZOYYKBzEblVWdXkta245Y0k/" type="text/javascript"> </script> <!--javascript-->
<script src="https://googledrive.com/host/0B4ZBZOYYKBzEblVWdXkta245Y0k/" type="text/javascript"> </script> <!--javascript-->
-
     <style>
+
<script>
 +
        $(document).ready(function($) {
 +
 
 +
/*load in the sidebar*/
 +
$('.left_wrap').load('https://googledrive.com/host/0B4ZBZOYYKBzEclFHMmpZcVlydmc');
 +
 
 +
          });
 +
     </script>   
 +
<style>
              
              
          
          
Line 21: Line 29:
   <!-- <div class="logo-wrap"><img src="https://googledrive.com/host/0B4ZBZOYYKBzEUlI3ZDU2OGRrc1E" id="penn"/></div><!--penn logo-->
   <!-- <div class="logo-wrap"><img src="https://googledrive.com/host/0B4ZBZOYYKBzEUlI3ZDU2OGRrc1E" id="penn"/></div><!--penn logo-->
      
      
-
    <ul class="navbar">
 
-
        <a href="https://2013.igem.org/Team:Penn"><li>home</li></a>
 
-
                <li class="dropdown" id="project">
 
-
                  <a href="#" class="active" data-toggle="dropdown">project<div class="arrow">></div> <b class="caret"></b></a>
 
-
                  <ul class="dropdown-menu" id="drop-menu1">
 
-
                 
 
-
                    <a href="https://2013.igem.org/Team:Penn/Project"><li>project</li></a>
 
-
                    <a href="https://2013.igem.org/Team:Penn/Parts"><li >parts</li></a>
 
-
                    <a href="https://2013.igem.org/Team:Penn/Modeling"><li class="active" style="background-color: rgb(200,200,215);">modeling</li></a>
 
-
                    <a href="https://2013.igem.org/Team:Penn/Safety"><li>safety</li></a>
 
-
                  </ul>
 
-
                </li>
 
-
                <li class="dropdown" id="about">
 
-
                  <a href="#" class="dropdown-toggle" data-toggle="dropdown">about<div class="arrow">></div>  <b class="caret"></b></a>
 
-
                  <ul class="dropdown-menu" id="drop-menu2">
 
-
                  <a href="https://2013.igem.org/Team:Penn/Team"> <li>team</li></a>
 
-
                  <a href="https://2013.igem.org/Team:Penn/Sponsors"> <li>sponsors</li></a>
 
-
                    <a href="https://igem.org/Team.cgi?id=1128"><li>official team profile</li></a>
 
-
                </li></ul>
 
-
 
-
                  <a href="https://2013.igem.org/Team:Penn/HumanPractices"><li>human practices</li></a>
 
-
<a href="https://2013.igem.org/Team:Penn/Notebook"><li>notebook</li></a>
 
-
        </ul>
 
      
      
      
      
-
     <div class="section-title" style="">modeling</div>
+
   
 +
     <div class="section-title" style="left: 20px;">modeling</div>
     </div>  
     </div>  
     <div class="section1" style="background-position: top;">
     <div class="section1" style="background-position: top;">
         <div class="text">
         <div class="text">
-
              
+
             <b><center><h1>
 +
MaGellin
 +
</b></center></h1>
 +
<br>
 +
<b><center>
 +
 
 +
Open Source Automated, Quantifiable DNA Analysis for our Assay
 +
</b></center>
 +
<br>
 +
MaGellin is a MATLAB script that uses computer vision algorithms to calculate the location and intensity of DNA bands. It also has a bioinformatics module to compare the lengths of bands with the expected lengths, based on the methylation sensitivity of the enzymes and the plasmid of the sequence. So, MaGellin is more than another gel quantifier - it interprets the biological meaning of the band lengths and returns experimentally relevant analyses. MaGellin is crucial for our workflow because it allows for clear input/output. Since our restriction digests always yield bands in predictable locations, MaGellin eliminates user bias and standardizes data sets across trials and labs, accelerating the pace of discovery.
 +
<br>
 +
<br>
 +
MaGellin converts gel images into standardized data sets, making data analysis quick, easy and unbiased.
 +
<br>
 +
<img src="http://s21.postimg.org/z98hqbrdj/gellin.png">
 +
<br>
 +
<br>
 +
A User-friendly GUI that is easy to navigate makes it ideal for first time users.
 +
<br>
 +
<img src="http://s8.postimg.org/5cd9z4b79/gellingui.png">
 +
<br>
 +
<br>
 +
The bioinformatics module simulates DNA digestion, so you know what bands to expect before even touching a pipette.
 +
<br>
 +
<img src="http://s14.postimg.org/6dwg73o5t/gellinbioinfo.png">
 +
<br>
 +
<br>
 +
Computer vision algorithm calculates location and intensity of DNA bands.
 +
<br>
 +
<img src="http://s16.postimg.org/6smb69xt1/gellinvision.png">
 +
<br>
 +
<br>
 +
SkyDrive provides open access to data and encourages collaborations. MaGellin is the interface to our assay, and it acts to abstract our plasmid system the same way a programming language abstracts computer hardware. 
 +
<br>
 +
<img src="http://s18.postimg.org/fusjsrq1l/gellindrive.png">
 +
 
         </div>
         </div>
     </div>
     </div>

Latest revision as of 10:19, 27 September 2013

modeling

modeling

MaGellin


Open Source Automated, Quantifiable DNA Analysis for our Assay

MaGellin is a MATLAB script that uses computer vision algorithms to calculate the location and intensity of DNA bands. It also has a bioinformatics module to compare the lengths of bands with the expected lengths, based on the methylation sensitivity of the enzymes and the plasmid of the sequence. So, MaGellin is more than another gel quantifier - it interprets the biological meaning of the band lengths and returns experimentally relevant analyses. MaGellin is crucial for our workflow because it allows for clear input/output. Since our restriction digests always yield bands in predictable locations, MaGellin eliminates user bias and standardizes data sets across trials and labs, accelerating the pace of discovery.

MaGellin converts gel images into standardized data sets, making data analysis quick, easy and unbiased.


A User-friendly GUI that is easy to navigate makes it ideal for first time users.


The bioinformatics module simulates DNA digestion, so you know what bands to expect before even touching a pipette.


Computer vision algorithm calculates location and intensity of DNA bands.


SkyDrive provides open access to data and encourages collaborations. MaGellin is the interface to our assay, and it acts to abstract our plasmid system the same way a programming language abstracts computer hardware.

Retrieved from "http://2013.igem.org/Team:Penn/Modeling"