[Acedb-soft] BIRCH: ACEDB organizes software documentation

Brian Fristensky frist at cc.umanitoba.ca
Mon Oct 24 12:34:02 EST 2005


Readers of this group may be interested in knowing that the
BIRCH bioinformatics platform employs ACEDB as the 
database manager for all software documentation files,
giving the user a one-stop view of all documentation for
all programs.  
The Python program htmldoc.py automatically creates
web pages from the birchdb database. Web pages organize
programs by Category, Package, and also a Program Index.
A tutorial with screenshots showing how local documentation
is merged with core BIRCH documentation is found at

http://home.cc.umanitoba.ca/~psgendb/birchadmin/addprog/localdocs.html

Below is a more general description of the most recent
release of BIRCH

---------------------------------------------------------------
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. 



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