[Biodevelopers] Mathematica in bioinformatics and computational biology

[Dhirendra Pal Singh]

I tried it.
Its there.
Dp


Asen Nenov wrote:
> http://www.higgins.ucdavis.edu/biomath.php
> 
> ERR 404 - no such page..
> 
> 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
>>
>> 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
>>
>>
>>
>>
>>
>> _______________________________________________
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>>
>>
>>  
>>
> 
> 
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