biok (http://www-alt.pasteur.fr/~letondal/biok/) is a prototype of a programmable 
application for biologists. Its purpose is twofold: to analyze biological data 
such as biological DNA or protein sequences, and to support tailorability and 
extensions by the end user through an integrated programming environment. 

The central analysis tools of the system are an alignment editor built on
a spreadsheet with programmable visualization features, a sequence
editor, and a plot editor. A tree editor is under development. biok
encompasses a Pise interface generator and is able to run EMBOSS
applications. It is an integration environment, based on on user
interface building features and on a dataflow model which enables to
connect all these components together by formulas.

It is written in XOtcl, an object extension of Tcl and, thanks to
Tcl introspection tools, selected graphical objects' source
code is available at the method level directly through the user
interface. Dataflow implementation and programming tools (trace and
debugging) rely on XOtcl features such as filters, mixins,
object-based programming and design patterns. 

The design of this tool follows human-computer interaction principles,
such as task-oriented programming, programming in the user interface,
cooperative and participatory programming. The prototype has been
presented to individual biologists, evaluated in a workshop, and used
by students for their project. 

-- 
Catherine Letondal -- Pasteur Institute Computing Center