seeking Java code for molecular biology apps

Joe Ryan jfryan at NHGRI.NIH.GOV
Mon Apr 26 17:22:34 EST 1999


A search at AltaVista on "+java +bioinformatics" returned 16949 web pages
so that might be a good starting point for you.  
You may find Tom Christiansen's complex datastructure modules and     
implementations on CPAN helpful for future Perl projects...

Here are some Bioinformatic Java Applications from my bookmarks...

The CBIL group at the University of Pennsylvania maintains bioWidgets for Java

Don Gilbert has written some nice Applications

Lincoln Stein has written a Java interface to ACEDB

JaMBW, the Java based Molecular Biologist's Workbench


Joseph Ryan
Perl Freak
National Human Genome Research Institute

On Mon, Apr 26, 1999 at 04:06:29PM -0400, George Armhold wrote:
> 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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