PAG-XIV (CP020) How To Build An In-House Bioinformatics System Tailored To Your Local User Community

Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

Computer: Poster and Demo

CP020

How To Build An In-House Bioinformatics System Tailored To Your Local User Community

Department of Plant Science University of Manitoba Winnipeg, MB CANADA R3T 2N2

The word 'system' implies many parts working together in a
coordinated fashion. While installing programs and databases can be a
major effort, transforming them from a mere collection into an
integrated system is far more difficult.

The BIRCH system (http://home.cc.umanitoba.ca/~psgendb)
makes it easy to find and use almost any program, data or document.
The core distribution includes software for DNA, protein, and
molecular marker data.

For end users:

The GDE graphic interface [Smith et al., 1994] makes it easy to create ad hoc data pipelines using
output from one program as input for another.

Locally-installed programs and
databases can be added transparently, without re-compiling GDE.

Web documentation from the BIRCH
core and local documents are unified in a single database.

Tutorials are task-oriented, rather
than program-oriented.

For the sysadmin:

Install wizard automates
installation, configuration and updates.

Local customizations automatically
re-integrated into BIRCH during updates.

Central configuration: everything
works the same for all users.

OS-independent datafiles,
documentation and scripts are installed separately from OS-dependent
binaries. BIRCH automatically finds the binaries for each host (eg.
Solaris, Linux)

All components are freely-available
software.

Scaleable from a single PC to a campus-wide system

Web applications are awkward to use and are intractable to
automation for large projects. When BIRCH is installed along with
desktop and office applications, the result is a seamless system on a
single desktop. Because BIRCH is network-centric, any user can do
any task from anywhere.