seeking Java code for molecular biology apps

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


George, 

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...
  http://www.perl.com/CPAN/authors/id/TOMC/scripts/CS-Talk/source/dstructs

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

The CBIL group at the University of Pennsylvania maintains bioWidgets for Java
    http://www.cbil.upenn.edu/bioWidgets/index.html

Don Gilbert has written some nice Applications
    http://iubio.bio.indiana.edu/soft/molbio/java/apps/

Lincoln Stein has written a Java interface to ACEDB
    http://stein.cshl.org/jade/

JaMBW, the Java based Molecular Biologist's Workbench
    http://www.embl-heidelberg.de/JaMBW/

Regards,

Joe
--
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]
> 




More information about the Bio-soft mailing list