Team:NYU/Programming

Contents 1 About this Page 2 Biobricking Primers 3 Overlap Oligo Maker 4 Manipulation of Protein Structures 5 Processing Visualization

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.

• Finally got the CGI working - click below or go [http://openwetware.org/images/a/a7/Biobrickprimers.txt here for the source code]

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.

• I'm a CGI machine! [http://openwetware.org/images/6/67/Overlapoligos.txt Here is the source code.] or click below for an interactive version.

Manipulation of Protein Structures

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 [http://www.processing.org Processing] language 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.