Databases and Systems

6
end databases and front-end viewers and analysis tools. In contrast to OPM and
BioKleisli, CORBA does not so much offer a standard data model as provide a
mechanism for isolating system components from the design constraints that might be
imposed by choosing particular data models. The Biowidgets article by
Crabtree et al describes an approach to modular software development for
bioinformatics visualization. Biowidgets represents an attempt to apply that modular
design philosophy to the problem of data visualization.
The ACE database manager, described by Jean and Danielle Thierry-Mieg,
is the database kernel of the ACEDB system developed by Jean Thierry-Mieg and
Richard Durbin for the C.elegans genomic database, and subsequently reused widely
by many other projects. The tremendous success of ACEDB over the years can be
attributed to a number of factors, including its biologist-friendly user interface, the
ease with which data can be entered into it, the ease with which its schema can be
modified, the ease with which new visualization and analysis routines can be added
to it, the extensive genomics knowledge incorporated into its standard schema and
software, and its price (free!). At the core of the system is a somewhat non-standard
object-oriented DBMS which over a reasonably wide range of database sizes can
outperform most commercial relational databases at tasks such as retrieving an object
detail view, pulling up annotated sequence, or displaying a genetic map. It is
heartening, in an era when DBMS development has been taken over by large
corporations wielding enormous programming teams, to see that a tiny team of
talented individuals can still write a system which outperforms the commercial
products in many respects.
Laboratory information management systems (LIMS) are a species of
software remote from the experience of many bioinformatics practitioners, for whom
data are something that automatically appear in databases. Those of us who have had
occasion to wander into the more upstream regions of the data production process
encounter a world of robots, sequencing machines, bench biologists, pipettes and 96well
plates. This world turns out to be full of interesting and exotic software
engineering challenges which are not well served by the current generation of
commercial solutions. Goodman et al present an elegant and general approach to the
problem of laboratory process workflow which they developed for use in the
Whitehead Genome Sequencing Center.
The articles in this book constitute a very incomplete sample of the
interesting systems out there. Notable gaps include databases for such important
model organisms as yeast, C.elegans and Arabidopsis as well as a number of
microbial databases; databases on protein sequences, families, and 3D structures;
expression profile databases, and transcription factor and promoter databases.
Starting points for finding such resources include [ 17,18].
One final note: in keeping with the rapid pace of change in this field, many
ofthe authors are no longer at the institutions where the work was performed, and in
some cases the addresses shown are out of date. During the period when this book
was being written (1997 -98), a number of the authors (myself, Markowitz et al, Karp,
Etzold) moved from public sector to private sector positions, and several of the