[Biodevelopers] Mathematica in bioinformatics and computational biology

[Andrew A. de Laix]

Hi,

For those of you who are studying bioinformatics, Brian Higgins at UC Davis
has put together a series of Mathematica notebooks illustrating many of the
basic concepts and algorithms including Mathematica implementations.  You
can read more about his notebooks and download them here:
http://www.higgins.ucdavis.edu/biomath.php.  The code in these notebooks
would also be good for those interested in using Mathematica to prototype
informatics algorithms.  

Unfortunately, one area were Mathematica doesn't live up to its full
potential is string parsing.  At this time it doesn't support regular
expressions (we are actively working to add that feature).  Higgins gets
around this by using Mathematica's superlative pattern matching capabilities
on character lists, but I don't know how much of a performance hit one takes
on account of that.  I'd be interested from hearing from you professionals
on that score. 

An alternative is to use J/Link, Mathematica's Java integration API to link
to bioinformatics Java libraries like bioJava (http://biojava.org).  J/Link
provides an amazingly easy interface to Java classes (so easy I can use it,
and that is saying something ;-)).  If fact, if any of you all are
interested in contributing a little time to a project to create a J/Link
interface to bioJava, please drop me a line.  This would be for a free and
open package, and not a commercial project. 

For those of you who would like to know more about Mathematica, everything
you could ever want to know, and a lot more, can be found at
http://www.wolfram.com.  If you are new to Mathematica, start at
http://www.wolfram.com/products/mathematica/index.html for a comprehensive
overview.  The complete documentation for Mathematica (and all other Wolfram
products) can be found here http://documents.wolfram.com/.  When you are
ready to kick the tires, you can download a trial version
http://www.wolfram.com/products/mathematica/trial.cgi, or why not just buy
your own copy at http://store.wolfram.com :-).

Andrew

Andrew A. de Laix, PhD
Business Development Manager
Wolfram Research, Inc.
phone: 510-655-5806
email: delaix at wolfram.com
web: http://www.wolfram.com