Team:Penn/MaGellinSoftware

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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.  
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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>
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MaGellin converts gel images into standardized data sets, making data analysis quick, easy and unbiased.
 
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<center><b>Protocol</b></center>
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A User-friendly GUI that is easy to navigate makes it ideal for first time users.
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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.
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2. Press the <b>Analyze</b> button.
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The bioinformatics module simulates DNA digestion, so you know what bands to expect before even touching a pipette.
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3. The Magellin Software Package will calculate the intensity and position of each band and produce a graph. Save your results.
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4. Collaborate with your fellow scientists by sharing your results on SkyDrive.
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Computer vision algorithm calculates location and intensity of DNA bands.
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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.
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<br><br><a href="https://2013.igem.org/Team:Penn/MaGellinFutureDirections"><i>Read about our future directions!</i></a>
<br><br><a href="https://2013.igem.org/Team:Penn/MaGellinFutureDirections"><i>Read about our future directions!</i></a>
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Revision as of 01:25, 28 September 2013

modeling

The MaGellin Software Package
Open Source Automated, Quantifiable DNA Analysis for our Assay


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.

INSERT picture of gel with arrow pointing to picture of graph, but not that blurry one we have now.

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.
INSERT picture of filled-out GUI.
2. Press the Analyze button.
INSERT picture of analyze button on GUI with mouse hovering over it. 3. The Magellin Software Package will calculate the intensity and position of each band and produce a graph. Save your results.
INSERT picture of graph
4. Collaborate with your fellow scientists by sharing your results on SkyDrive.


Read about our future directions!

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