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BIRCH: Comprehensive bioinfo. system - News

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BIRCH Version 2.0
Submitted by Brian Fristensky; posted on Thursday, October 05, 2006
o Some Linux distributions (eg. Fedora) do not have Java, but rather,
a GNU bytecode interpreter called gij. gij did not work correctly
with ANY Java application tested. The solution is to install
the real Java from Sun, and make sure that java (and not gij)
is in the $PATH. Instructions for this workaround have been
added to the Pre-installation instructions.
o Fixed some problems with fasta2install.csh and fasta3install.csh.
On some systems, these scripts did not correctly detect the
available C-compilers.
o A major re-organization and rewrite has been done for
documentation linked from the BIRCH home page under
the name "Using Unix from Anywhere". The new documentation
goes into more depth on using commandline clients, VNC,
X-terminals, and other thin clients.
o The re-organization of documentation has prompted the addition
of a new script ( to the update procedure used
by During an update, files present in
local-generic/public_html/remote, but not in local/public_html/remote,
will be copied to local/public_html/remote. This will probably be expanded to
encompass other files and directories in a later release.
o Bluejay has been upgraded to the version dated Aug. 25, 2006.
o local-generic/platform.source and platform.profile.source now contain
code for setting BIRCH_PLATFORM automatically, using the Unix 'uname'
command. This code is commented out, and must be uncommented to take
effect. This feature is still being tested.
o For distance phylogeny methods run by mGDE, restdist.csh failed to
generate multiple datasets for resampling methods (ie. bootstrapping,
jacknifing etc.) This problem only affected molecular marker
distance methods, and not sequence distance methods. This
problem has been fixed.
BIRCH Version A1.99
Submitted by Brian Fristensky; posted on Wednesday, June 28, 2006
BIRCH Version A1.99

o miniBIRCH is now supported by birchconfig, the graphic
install wizard. The install procedure for minibirch is
almost identical to that for a complete BIRCH installation,
with the addition that for miniBIRCH, the New Install window
will have an additional 'miniBIRCH Master Directory' field.
o New: ArrayNorm - Normalize raw gene array data, prior to analysis
o New: TIGR-TM4 Microarray programs:
ExpressConverter - converts array data to TIGR format
MIDAS - Normalization and analysis
MEV - Multi-experiment viewer for data mining
o New: weighbor: Neighbor-Joining program which produces more reliable
trees than traditional NJ. Available as an option in GDE.
o Documentation pages for Packages and Programs now contain links
to a glossary page which gives definitions for each field on the
o Treetool, the tree editor, is now available for all platforms.
Previously, colormap issues prevented it from running on Solaris.
Thanks to Eric Linton for fixing this problem.
o readseq has been upgraded to version 2.1.23.
o GDE has been upgraded to version 2.4.5. GDE 2.1.5, wrote some
temporary files to /usr/tmp, which is not present on some Debian
systems. GDE 2.4.5 writes these files to /tmp, which is present on all
Unix and Linux systems.
o dapple has been removed from the BIRCH core distribution.


The latest release of BIRCH (A1.99) is available at the
BIRCH Web site

under the link 'BIRCH Administrator's Guide'.

BIRCH A1.98 - updates and new features
Submitted by Brian Fristensky; posted on Monday, April 17, 2006
Submitter BIRCH Release A1.98

o Bluejay has been upgraded to the version dated Jan. 27, 2006
o Artemis has been upgraded to v.8
o Taverna has been upgraded to v. 1.3.1. This version fixes problems
which caused Taverna to crash with Java 1.5.
o GDE has been upgraded to macGDE v. 2.1.5. In this version, the
HELP button in each menu launches a standalone document viewer,
rather than displaying the documentation in the menu itself.
o The CopyOut and PasteIn commands for dGDE, GDE, mGDE and tGDE now
use separate clipboard files. For example, the PastIn for tGDE will
past in the most recent clipboard contents from tGDE, and PasteIn
for dGDE will paste in the most recent clipboard contents from dGDE.
o Leash has been upgraded to version 2.2. This version includes
new command line parameters, -mpil and -mpif, which make it possible
for Leash to take lists of data as input for SeqHound methods
which only allow a single data item (eg. SHoundSequenceLength).
Previously, leash had to be called for each item in the list.
A number of dGDE method calls have been updated to take advantage
of the increased efficiency of these parameters.

o Added new features to BACHREST that gives the user more ways to narrow
the list of enzymes and digests shown in the output. Searches can be limited
to enzymes that generate 5' protruding, blunt or 3' protruding ends, or that
have either symmetric or asymmetric recognition sequences. The parameters
LEASTFRAGS and MOSTFRAGS also allow you to only print digests with at least
LEASTFRAGS fragments, or at most MOSTFRAGS. It is also possible to
keep the output file small by setting PRINTFRAGS. When the number of fragments
in a digest exceeds PRINTFRAGS, MULTIDIGEST will only print the number
of fragments, rather than printing all of the fragments themselves.
Finally, BACHREST now prints the values of these parameters in the
header lines of the output file.

The maximum sequence size allowed by BACHREST has been increased to
20,000,000, allowing most bacterial genomes to be read. However,
for very large sequences, BACHREST must be used at the command line. GDE
will only read sequences that are 750K or smaller.

To avoid conflict with the Solaris 10 digest command, DIGEST has been
renamed as MULTIDIGEST. MULTIDIGEST has been updated to read the
new BACHREST output file format.

Also, see what else is new with BIRCH, from the
presentation at the Plant and Animal Genome Conference XIV:



The latest release of BIRCH (A1.98) is available at the
BIRCH Web site

under the link 'BIRCH Administrator's Guide'.

BIRCH now available for Solaris/AMD64
Submitted by Brian Fristensky; posted on Tuesday, January 03, 2006
BIRCH Release A1.96

BIRCH now supports the Solaris/AMD64 platform.

With the latest release, binaries for most BIRCH
core programs are now available for Sun's Solaris/AMD64
machines. In mixed platform environments, BIRCH users
can now run most BIRCH applications transparently with
respect to whether they are logged into a Linux-Intel,
Solaris-Sparc or Solaris-AMD64 host.


The latest release of BIRCH (A1.96) is available at the
BIRCH Web site

under the link 'BIRCH Administrator's Guide'.

A1.96 Release Notes
December 29, 2005
o To simplify the process of making BIRCH documentation Web-accessible,
the birchconfig URL Builder has additional suggested choices for
possible locations of the BIRCH web site and Home directories.
o BIRCH now supports the solaris-amd64 platform. Some programs
are not available for solaris-amd64, including mapmaker and primer3.
o birchconfig.csh has been replaced by Since some
systems do not have csh as a standard part of the system (and
we assume that all Unix systems have sh) this script is better
as an sh script. now checks for the presence
of csh, python and java, and prints error messages if these
are not present. All three must be present to run birchconfig.jar.
o UNINSTALL-birch.csh has been replaced with

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