Team:NYU/Programming

From 2010.igem.org

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Sung and Seok Hwan also made a [http://www.processing.org Processing] language [[Image:Processing.jpg|200px|left]] based visual aid describing the Immunoyeast system. Go [http://www.russelldurrett.com/processing here] to take a look at it, and feel free to play around with the code!  
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Sung also made a [http://www.processing.org Processing] language [[Image:Processing.jpg|200px|left]] based visual aid describing the Immunoyeast system. Go [http://www.russelldurrett.com/processing here] to take a look at it, and feel free to play around with the code!  
We will also have an interactive touch based installation of the visualization for you to play with at the jamboree.
We will also have an interactive touch based installation of the visualization for you to play with at the jamboree.
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[[Image:Cave_composite.png|300px|left]]

Revision as of 03:17, 28 October 2010



NYU OverviewSideF 2.png

Contents

About this Page
  • Competent programming skills are quickly becoming a necessity for working in biology. Because most of our team members had never had exposure to a programming environment, we decided to use the obstacles presented in our iGEM experiments as cause for learning the Perl programming language and produced some simple scripts that could do routine iGEM labors for us. Here are some examples:


Biobricking Primers
  • This script allows the user to input a DNA sequence and outputs the primers necessary for biobricking that sequence via PCR. The script calculates Tm but does not (yet) consider primer dimers.


Overlap Oligo Maker
  • Some very fast and efficient DNA assembly methods require parts to overlap on the ends of their sequences. This script will take two DNA sequences and output the oligos (and their Tms) one would need to PCR constructs with overlapping ends.



Manipulation of Protein Structures
Screen shot 2010-10-27 at 10.19.59 PM.png

In order to more fully understand certain parts of our system and to use the ridiculously amazing CAVE system at Cornell Med School, we decided to explore the 3D structures of the proteins involved in our system. Because the mechanism of Cre recombination is difficult to understand, we dove into the structures available on the Protein DataBase (PDB) and explored details of the mechanism. We were able to locate the active sites of the protein, isolate the catalytic residues, locate the vanadium cofactors and, in all, gain a better understanding of the protein's function. Check out some pictures below!




Processing Visualization
Sung also made a Processing language
Processing.jpg
based visual aid describing the Immunoyeast system. Go here to take a look at it, and feel free to play around with the code!

We will also have an interactive touch based installation of the visualization for you to play with at the jamboree.