[Biodevelopers] Mathematica in bioinformatics and computational biology

[Asen Nenov]

http://www.higgins.ucdavis.edu/biomath.php

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Regards
Asen Nenov
Sofia, Bulgaria

Andrew A. de Laix wrote:

>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
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>would also be good for those interested in using Mathematica to prototype
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>informatics algorithms.  
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>
>
>Unfortunately, one area were Mathematica doesn't live up to its full
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>potential is string parsing.  At this time it doesn't support regular
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>expressions (we are actively working to add that feature).  Higgins gets
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>around this by using Mathematica's superlative pattern matching capabilities
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>on character lists, but I don't know how much of a performance hit one takes
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>on account of that.  I'd be interested from hearing from you professionals
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>on that score. 
>
>
>
>An alternative is to use J/Link, Mathematica's Java integration API to link
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>to bioinformatics Java libraries like bioJava (http://biojava.org).  J/Link
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>provides an amazingly easy interface to Java classes (so easy I can use it,
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>and that is saying something ;-)).  If fact, if any of you all are
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>interested in contributing a little time to a project to create a J/Link
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>interface to bioJava, please drop me a line.  This would be for a free and
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>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
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>Business Development Manager
>
>Wolfram Research, Inc.
>
>phone: 510-655-5806
>
>email: delaix at wolfram.com
>
>web: http://www.wolfram.com
>
>
>
>
>
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>