Databases and Systems

Introduction
21 BIOWIDGETS:REUSABLE
VISUALIZATION COMPONENTS
FOR BIOINFORMATICS
Jonathan Crabtree, Steve Fischer, Mark
Gibson and G. Christian Overton
Center for Bioinformatics, University of Pennsylvania,
Philadelphia, PA 19104
Genome centers around the world are ramping up to the sequencing throughput
required to bring the first phase of the Human Genome Project to a close. It is more
apparent than ever that bioinformatics support must play an integral role in genomescale
mapping and sequencing projects. As genomics data is collated into
information management systems, it furthermore must become available to scientists
in a form that facilitates their comprehension of it. Interactive data visualization
components provide a way to fulfill this need
In large part because of the limited resources often allocated to bioinformatics in
the past, those responsible for designing and implementing laboratory information
systems have had to make do with what they could get, particularly in terms of
obtaining software. As Goodman put it, “the choices that face the architect of a
genome information system today are: (i) build it yourself so that it does exactly what
you want, or (ii) adopt someone else’s system and live with most of its quirks and
limitations” [ 1].
The solution to the problem of limited resources is simple in principle: design
systems as collections of interoperable components and share those components
freely. The tacit assumption in this approach is that smaller, more modular programs
will be able to avoid the quirks and limitations that tend to be the hallmarks of large
“monolithic” systems. And even if some components fall short in this regard, making
use of them is, by definition, not an all-or-nothing proposition. This is the motivation
behind the bioWidgets project, an effort to create and share graphical user interface