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BIRCH Version 2.2
BIRCH: A user-oriented, locally-customizable, bioinformatics system
Brian Fristensky
BMC Bioinformatics 2007, 8:54 (9 February 2007)
http://www.biomedcentral.com/1471-2105/8/54/abstract
BIRCH (Biological Research Computing Hierarchy) is an organizational
framework for delivering bioinformatics resources to a user group,
scaling from a single lab to a large institution. The BIRCH core
distribution includes many popular bioinformatics programs, unified
within the GDE (Genetic Data Environment) graphic interface. Of equal
importance, BIRCH provides the system administrator with tools that
simplify the job of managing a multiuser bioinformatics system across
different platforms and operating systems.
The latest release of BIRCH (2.2) is available at the
BIRCH Web site
http://home.cc.umanitoba.ca/~psgendb
under the link 'BIRCH Administrator's Guide'.
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New in the current release:
o Fixed an error in birchconfig.sh which failed to detect when python
was absent from the $PATH.
o NCBI has split the GenBank ACCESSION index among several files. gbupdate
has been revised to automatically downoad and install all of these files.
o Taverna has been upgraded to version 1.5.1.
o The Network Entrez client no longer works, and has not been
supported by NCBI for some time. It has been removed from BIRCH.
o NCBI Sequin has been upgraded to version 7.35.
o The Phylip TREEDIST program has been added to tGDE.
o In GDE, if FEATURES is launched with no sequences selected, getob
would go into an infinite loop. This has been fixed in FEATURES.
o MrBayes 3.1 has been added to BIRCH. MrBayes uses Bayesian methods
for phylogenetic analysis of nucleic acids, proteins, molecular
marker and discrete morphology data.
o On some linux-intel systems, sequin would not run because it could
not find two library files (libXm.so.2,libXp.so.6). Sequin is now run
through a wrapper script that adds this file to the LD_LIBRARY_PATH.
o The Phylip PARS program has been added to mGDE
o Bluejay has been updated to version 0.701
