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Using Mathematica to Teach Bioinformatic Skills

Brian G. Higgins
Organization: University of California, Davis
Department: Department of Chemical Engineering & Materials Science

2003 Mathematica Developer Conference
Conference location


In this talk I will discuss how Mathematica can be used to manipulate and process biological data using built-in string manipulation functions. These capabilities do not seem to be well appreciated by the bioinformatics community who traditionally have used Perl as their programming environment. Recent developments have made Mathematica an attractive programming environment for managing and analyzing biological data. For example, with the J/Link toolkit it is now possible to integrate Mathematica and Java so that modules from BioJava can be accessed directly from Mathematica, thereby extending the Mathematica computing environment for bioinformatics. One of Mathematica's newest features is its ability to import/export XML data, which can be parsed and manipulated using Mathematica's SymbolicXML function.

In this presentation I will give a brief overview of several bioinformatics problems and then I will show how Mathematica can be used to teach programming skills for bioinformatics. I will discuss the parsing and management of biological data from various sources (GenBank, PDP, BLAST). I will also demonstrate how Mathematica can be used to manipulate DNA and protein sequences.

The notebooks for this talk are available at http://www.higgins.ucdavis.edu/biomath.php

*Science > Biology
*Wolfram Technology > Linking Technology > J/Link
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HigginsWRIDev_03b.nb (369.2 KB) - Mathematica Notebook