Splicing UNIX into a Genome Mapping Laboratory
Lincoln Stein, Andre Marquis, Ert Dredge, Mary Pat Reeve,
Mark Daly, Steve Rozen, Nathan Goodman
Whitehead Institute for Biomedical Research
One Kendall Square
Cambridge, MA 02139
Abstract
The Whitehead Institute/MIT Center for Genome Research is responsible
for a number of large genome mapping efforts, the scale of which
create problems of data and workflow management that dictate reliance
on computer support. Two years ago, when we started to design the
informatics support for the laboratory, we realized that the fluid and
ever- changing nature of the experimental protocols precluded any
effort to create a single monolithic piece of software. Instead we
designed a system that relied on multiple distributed data analysis
and processing tools knit together by a centralized database. The
obvious choice of operating systems was UNIX. In order to make this
choice palatable to the laboratory biologists--who rightly consider it
their job to do experiments rather than to interact with computers,
and who have come to expect all software to be as intuitive and
responsive as the Apple Macintoshes on their desks--we designed a
system that runs automatically and essentially invisibly. Whenever it
is necessary for the informatics system to interact with a member of
the laboratory we have carefully chosen a user interface paradigm that
best balances the user's expectations against the system's
capabilities. When possible we have chosen to adapt familiar software
to our user interface needs rather than to write user interfaces from
scratch. We've managed to hide the power of UNIX behind the innocuous
personal computer-based front ends our users know and love, using
techniques that should be applicable in other environments as well.
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