A beta release of bioTkperl is now available for distribution. This is
a port of David Searls' bioTk Tcl/Tk widgets to Tk/Perl, with some
enhancements. Not all of the components have been ported yet, but the
ones that have are pretty stable.
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What is bioTk?
From the bioTk home page (http://www.cbil.upenn.edu/~dsearls/bioTk.html):
"bioTk is a library of widgets and utilities designed to support the
creation of graphical user interfaces in the domain of computational
biology and genome informatics. The overarching philosophy behind
bioTk is componentry: that is, the creation of adaptable, reusable
software, deployed in modules that are easily incorporated in a
variety of applications, and in such a way as to promote interaction
between those applications."
The original implementation of bioTk was in Tcl, and is now at
release 1.3. A new release is being worked on. See the above URL
for details.
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What is bioTkperl?
bioTkperl is a port of the bioTk widgets/components to Tk/Perl, along
with some enhancements. Also, the bioTk components have been
reimplemented as Perl classes, so most procedures from the Tcl version
have been replaced with method calls on objects. However, particular
care was taken to keep the bioTk API compatible between the Tcl and Perl
implementations.
The current version is bioTkperl0.8, which includes a full Tk/Perl
implementation of the bioTk Sequence widget (for displaying DNA
sequences), and an almost complete implementation of the bioTk Map
widget (for displaying genomic maps), along with some added features.
It requires perl version 5.001m or higher and the Tk/Perl extension
version b6 or higher (if you only have access to an earlier version
of Tk/Perl, see the README for needed modifications).
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Where can you download bioTkperl?
Via anonymous ftp from fruitfly.berkeley.edu, in
/pub/bioTk/bioTkperl0.8.tar.gz.
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How about documentation and demos?
The Tcl version of bioTk includes extensive documentation, which applies
equally to the Perl version (the parts that have been ported), except for
differences noted in the README. The latest Tcl version can be found via
anonymous ftp at cbil.humgen.upenn.edu, under /pub/bioTk.tar.Z.
Ports of several tutorials/demos from the Tcl version (bioTk1.3) are
included in the distribution. The best way to get a feel for the
differences in using the Perl version is to look through the tutorial
demos, and compare them to sequence.tut and map.tut in the Tcl version.
In addition I have included a demo version of an application I have been
working on called AnnotP1. This has served both as a testbed for
bioTkperl and as a useful lab tool for analysis of P1 clones being
sequenced here at the Berkeley Drosophila Genome Center.
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Please feel free to send me comments, bug reports, etc.
Gregg Helt
gregg at fruitfly.berkeley.edu
