Team:Penn/MaGellinSoftware

From 2013.igem.org

(Difference between revisions)
 
(11 intermediate revisions not shown)
Line 1: Line 1:
<html lang="en">
<html lang="en">
<head>
<head>
-
    <title>modeling</title>
 
-
      <link href="https://googledrive.com/host/0B4ZBZOYYKBzEVHRaZEdUVGo5cjA" type="text/css" rel="stylesheet"/>
 
-
    <script src="https://googledrive.com/host/0B4ZBZOYYKBzETkFqdnhMeV9fMzA" ></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>
 
-
        $(document).ready(function($) {
 
-
/*load in the sidebar*/
+
    <title>Penn iGEM</title>
-
$('.left_wrap').load('https://googledrive.com/host/0B4ZBZOYYKBzEclFHMmpZcVlydmc');
+
    <link href="https://googledrive.com/host/0B4ZBZOYYKBzEVHRaZEdUVGo5cjA" type="text/css" rel="stylesheet"/> <!--css-->
-
          });
+
<script src="https://googledrive.com/host/0B4ZBZOYYKBzETkFqdnhMeV9fMzA" ></script> <!--jquery-->
-
    </script>  
+
-
<style>
+
-
           
+
-
       
+
      
      
-
          
+
<script>
-
     </style>
+
         $(document).ready(function($) {
 +
 
 +
$('.nav_wrap').load('https://googledrive.com/host/0B4ZBZOYYKBzEclFHMmpZcVlydmc');
 +
  });
 +
     </script>
</head>
</head>
 +
<body>
<body>
-
<img src="http://upload.wikimedia.org/wikipedia/en/d/d6/IGEM_official_logo.png" id="igem"/><!--igem logo-->
+
<div id = "banner_wrap">
-
<img src="http://collegediabetesnetwork.org/wp-content/uploads/2012/07/UPenn_logo1.png" id="penn"/> <!--penn logo-->
+
<div class = "banner"></div>
-
  <div class="left_wrap">
+
</div>
-
    </div> </div>
+
<div id = "nav_holder">
-
  <div class="section1" style="background-position: top;">
+
<div class = "nav_wrap"></div>
-
        <div class="text">
+
</div>
 +
</div>
 +
<div id="text">
 +
<div class = "textwrap">
             <b><center><h1>
             <b><center><h1>
The MaGellin Software Package
The MaGellin Software Package
Line 34: Line 31:
<i>Open Source Automated, Quantifiable DNA Analysis for our Assay</i>
<i>Open Source Automated, Quantifiable DNA Analysis for our Assay</i>
</center></h1>
</center></h1>
-
<br>
+
<br><br>
 +
For a detailed, graphical explanation of the MaGellin work flow, please download the <a href="https://dl.dropboxusercontent.com/u/11828463/MaGellin%20Spec%20Sheet.pdf">MaGellin Workflow Specifications Sheet</a>, which includes all of the steps in the MaGellin workflow.
 +
<br><br>
<b><center>
<b><center>
Overview
Overview
</b></center>
</b></center>
<br>
<br>
-
<center>
+
<div align=left>
The MaGellin Software Package 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 sequence of the plasmid. So, this program is more than another gel quantifier - it interprets the biological meaning of the band lengths and returns experimentally relevant analyses. The MaGellin Software Package is crucial for our workflow because it allows for clear input/output. Since our restriction digests always yield bands in predictable locations, user bias is eliminated and data sets are standardized across trials and labs, accelerating the pace of discovery. </center>
The MaGellin Software Package 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 sequence of the plasmid. So, this program is more than another gel quantifier - it interprets the biological meaning of the band lengths and returns experimentally relevant analyses. The MaGellin Software Package is crucial for our workflow because it allows for clear input/output. Since our restriction digests always yield bands in predictable locations, user bias is eliminated and data sets are standardized across trials and labs, accelerating the pace of discovery. </center>
<br>
<br>
-
INSERT picture of gel with arrow pointing to picture of graph, but not that blurry one we have now.
 
<br>
<br>
-
<br>
+
<b><center>
-
<center><b>Protocol</b></center>
+
Protocol
 +
</b></center>
<br>
<br>
1. Upload gel picture from restriction enzyme digest. Fill out all relevant information on the graphical user interface. Enter plasmid and target sequences and select restriction enzymes used. Enter descriptive names for gel and lanes if desired.
1. Upload gel picture from restriction enzyme digest. Fill out all relevant information on the graphical user interface. Enter plasmid and target sequences and select restriction enzymes used. Enter descriptive names for gel and lanes if desired.
<br><br>
<br><br>
-
INSERT picture of filled-out GUI.
+
<center><img src="http://farm6.staticflickr.com/5334/9974935346_ee05580236.jpg" width="319" height="285"></center>
<br><br>
<br><br>
2. Press the <b>Analyze</b> button.
2. Press the <b>Analyze</b> button.
<br><br>
<br><br>
-
INSERT picture of analyze button on GUI with mouse hovering over it.
+
<center><img src="http://farm4.staticflickr.com/3685/9975004403_c4ecb02a66.jpg" width="323" height="105"></center>
 +
<br><br>
3. The Magellin Software Package will calculate the intensity and position of each band and produce a graph. Save your results.
3. The Magellin Software Package will calculate the intensity and position of each band and produce a graph. Save your results.
<br><br>
<br><br>
-
INSERT picture of graph
+
<center><img src="http://farm8.staticflickr.com/7444/9975229953_4c5f81dc8b.jpg" width="409" height="319"></a>></center>
<br><br>
<br><br>
4. Collaborate with your fellow scientists by sharing your results on SkyDrive.
4. Collaborate with your fellow scientists by sharing your results on SkyDrive.
 +
<br>
 +
<br>
 +
 +
<center> <b> Details on the Software's Inner Workings</b></center>
 +
<br>
 +
Before the analysis is performed, the image is subject to various procedures intended to remove ambient noise in the data. These methods include determining the average amount of noise bias per row, and convolving the image with several standard filters. Next, the MaGellin software finds the lanes in the gel. This is accomplished by running an edge detection algorithm that uses the location of edges of individual bands to infer the location of the center of each lane.  The edge detection algorithm functions by treating edges as solutions to variational equations.  Once the center of each lane is determined, MaGellin is ready to perform its analysis. The user inputs the plasmid sequence in question, and MaGellin converts these values into vertical coordinates on the gel by performing a logarithmic regression on the length of the user input sequences, relying on the factory-included values for the lengths of the bands of the 2-Log ladder. Now MaGellin knows where to look, and it knows what it is looking for. All that’s left to do is run the analysis. MaGellin searches in the locations in question, and if a band of suitably high intensity is found, Magellin records the intensity at this location. If no such band is found, Magellin records the intensity as 0 to indicate that no band was found in the area. The data is then extrapolated into a graph with the relevant biological meaning. Usually, we perform our experiments in triplicate, so we can run a 2-way ANOVA.
<br><br>
<br><br>
-
<img src="http://s18.postimg.org/fusjsrq1l/gellindrive.png">
+
 
-
<br><br><a href="https://2013.igem.org/Team:Penn/MaGellinFutureDirections"><i>Read about our future directions!</i></a>
+
 
-
        </div>
+
<center>
 +
<a href="https://2013.igem.org/Team:Penn/MaGellinFutureDirections">Next&#8594;</a></center>
 +
</div>
     </div>
     </div>
      
      
-
 
+
</div>
    
    
</body>
</body>

Latest revision as of 04:23, 22 October 2013

Penn iGEM

The MaGellin Software Package

Open Source Automated, Quantifiable DNA Analysis for our Assay



For a detailed, graphical explanation of the MaGellin work flow, please download the MaGellin Workflow Specifications Sheet, which includes all of the steps in the MaGellin workflow.

Overview

The MaGellin Software Package 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 sequence of the plasmid. So, this program is more than another gel quantifier - it interprets the biological meaning of the band lengths and returns experimentally relevant analyses. The MaGellin Software Package is crucial for our workflow because it allows for clear input/output. Since our restriction digests always yield bands in predictable locations, user bias is eliminated and data sets are standardized across trials and labs, accelerating the pace of discovery.

Protocol

1. Upload gel picture from restriction enzyme digest. Fill out all relevant information on the graphical user interface. Enter plasmid and target sequences and select restriction enzymes used. Enter descriptive names for gel and lanes if desired.



2. Press the Analyze button.



3. The Magellin Software Package will calculate the intensity and position of each band and produce a graph. Save your results.

>


4. Collaborate with your fellow scientists by sharing your results on SkyDrive.

Details on the Software's Inner Workings

Before the analysis is performed, the image is subject to various procedures intended to remove ambient noise in the data. These methods include determining the average amount of noise bias per row, and convolving the image with several standard filters. Next, the MaGellin software finds the lanes in the gel. This is accomplished by running an edge detection algorithm that uses the location of edges of individual bands to infer the location of the center of each lane. The edge detection algorithm functions by treating edges as solutions to variational equations. Once the center of each lane is determined, MaGellin is ready to perform its analysis. The user inputs the plasmid sequence in question, and MaGellin converts these values into vertical coordinates on the gel by performing a logarithmic regression on the length of the user input sequences, relying on the factory-included values for the lengths of the bands of the 2-Log ladder. Now MaGellin knows where to look, and it knows what it is looking for. All that’s left to do is run the analysis. MaGellin searches in the locations in question, and if a band of suitably high intensity is found, Magellin records the intensity at this location. If no such band is found, Magellin records the intensity as 0 to indicate that no band was found in the area. The data is then extrapolated into a graph with the relevant biological meaning. Usually, we perform our experiments in triplicate, so we can run a 2-way ANOVA.

Next→