seeking Java code for molecular biology apps

George Armhold armhold at topside.rutgers.edu
Mon Apr 26 15:06:29 EST 1999

I am interested in hearing of any freely-available Java
implementations of software for molecular biology.  There is certainly
no dearth of Perl implementations, but I have seen very little done in
Java.  If you have written or have access to some code you would like
to share, please drop me a note.  Depending on the response I get, I
am considering setting up some sort of repository similar to what they
have done on http://bio.perl.org.

A few words about my motivation.  I am a programmer relatively new to
the field of Bioinformatics.  I've certainly written my share of Perl
code, and recognize its value.  At the present time, nothing can beat
Perl when it comes to parsing text, which is a task performed
constantly in this field.  However there are times when Perl is
downright frustrating to use due to its lack of support for complex
data structures.  The text-parsing abilities of Java are gradually
improving, and IMHO some applications would benefit from being written
in Java, even considering the relatively poor state of its
text-parsing code at the present moment compared to Perl.

George Armhold                    PGP Key: [02D2EBE5]
Rutgers University            Fingerprint: [51 8B A4 B0 7A 71 7C E7]
Bioinformatics Initiative                  [85 DE 13 99 0B 68 5F 92]

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