BIRCH Version 2.96

NEW:

New BioLegato instances for multiple DNA and protein alignments
Numerous usability improvements to BioLegato
bug fixes

BIRCH: A user-oriented, locally-customizable, bioinformatics system
Brian Fristensky
BMC Bioinformatics 2007, 8:54 (9 February 2007)
[Abstract] [ PDF]

BIRCH is

a comprehensive desktop bioinformatics system which comes with many of the commonly-used bioinformatics programs pre-installed
a framework of tools, files, and documentation for organizing and managing a bioinformatics core facility
an expandable system that allows you to merge 3rd party programs and documentation seamlessly into the standard BIRCH distribution

DOWNLOAD BIRCH NOW

New in the current release:

version 2.96 (May 21, 2013)

NEW and Updated Software applications:

Reorganization of multiple sequence alignment tasks - Tasks for displaying and working with multiple sequence alignments have been moved from bldna and blprotein into two new BioLegato interfaces: blnalign for aligned DNA or RNA sequences, and blpalign for aligned protein sequences. For example, if you run TCOFFEE from blprotein to produce a multiple alignment, the output will be sent to blpalign. blpalign can be used to run tasks that only make sense with aligned sequences, such as phylogenetic analysis or alignment display. By making BioLegato adhere more strictly to object-oriented organization, it becomes more difficult to accidentally run tasks such as phylogeny using unaligned sequences as input.

As part of this reorganization, mrtrans can now only be run from blpalign. This makes sense, because it forces the user to already have a protein alignment before trying to run mrtrans.
Local BIRCH web site now displays current release number and timestamp.
BioLegato.0.7.9

BioLegato can now Copy and Paste using the system clipboard. This makes it possible to paste seqences from documents, emails etc. into BioLegato, and to paste sequences from BioLegato into web programs.

numerous bug fixes and performance enhancements including:
ability to set the text in the BioLegato window header bar
ability to specify order of items in a PCD menu
fixes to table canvas selection
fixes to PCD's platform specificity options
import column headers from file in table canvas
better ability to skip improperly constructed PCD menus

the BIRCH Launcher and birchadmin tool now have a launcher for Release Notes.

The BLAST+ programs from NCBI replace blastcl3 (netblast). New menus in bldna and blprotein expand the number of search parameters that can be set.
SHUFFLE - The option to manually set a random seed when running SHUFFLE has been eliminated from bldna and blprotein. Instead, the script that runs SHUFFLE generates a random seed. Previously if the user didn't set a random seed each time, the same random sequence was generated each time the program was run. There is no obvious advantage to setting a random seed manually, so it is best to just do it automatically to be sure it gets done.
Calculation of protein statistics such as molecular weight, pI and amino acid frequencies is done by a new program gstat.py, launched from blprotein.
Archaeopteryx is a fully-featured program for drawing phylogenetic trees, and overlaying other sorts or data onto trees. Archaeopteryx is the successor to ATV. In future releases, Archaeopteryx will replace ATV. Currently, it can be launched from bltree.

DELETED applications:

NCBI blastcl3 (netblast)
prostat and dbstat have been replaced by gstat.py (see above)

Bug Fixes

On a multi-user BIRCH system on MacOSX, if a user who is not the owner of BIRCH clicks on the BIRCH launcher icon, they get a permission denied error. (Bugzilla #1178)
A bug has been fixed in BACHREST, which prevented setting the minimum and maximum length of restriction sequences to search for. (Bugzilla #1174)

version 2.95 (September 24, 2012)

NEW and Updated Software applications:

Cytoscape v2.8.3 - Visualize biochemical pathways
NCBI BLAST+ v2.2.26 - blastp,blastn, blastx, tblastn, tblastx, blast_formatter.

DELETED applications:

TM4 MIDAS

BIRCH

In this version of BIRCH, all BioLegato menus have been translated into a new menu language called BioPCD. BioPCD expands on the functionality of .GDEmenus, and this functionality will expand in future versions. The old .GDE menus are no longer used. During an upgrade from previous versions of BIRCH, your old GDE menus in $BIRCH/local will be translated into BioPCD. All future development of local menus should be done using BioPCD.
The following environment variables were previously deprecated,and are now removed from $BIRCH/admin/cshrc.source and $BIRCH/admin/profile.source : $DATA, $data, $DB, $db. In particular, it was discovered that then $DATA was set, it would prevent LibreOffice v3.3 and later from launching. See bugzilla.redhat.com Bug #834800.
NEW: birchadmin - This BioLegato tool performs administrative tasks for the BIRCH system. It can be launched from the BIRCH launcher. New functions include: htmldoc.py, customdoc.py, lbirchdb. birchadmin can only be run when logged in as the BIRCH administrator.
BIRCH launcher: The DNA, protein, and Multiple alignment menus have been merged into a single menu called "Sequence".
When launching bldna, blprotein, blmarker or bltree from the BIRCH launcher, the user is prompted to choose a working folder.
BioLegato - tool tips and icons have been added to most menus in BioLegato
BioLegato - it is now possible to set the title to appear at the top of a BioLegato window.

version 2.9

fixed a bug in the script that runs mrtrans that prevented mrtrans from running on some OSX systems.
ribosome - In the previous release, the new version of ribosome was omitted from OSX and linux-intel binaries. The new version is now available on all platforms. (Bugzilla# 1167)
The Phylip package has been upgraded to version 3.69.
The BIRCH launcher now prompts for a working folder when started at the command line. This results in all programs launched from the launcher opening in the working directory, rather than the home directory.
acedb - on some Mac and Linux systems, acedb failed to launch because of missing libraries. These libraries have been added to the current release. (Bugzilla #1156)
bioLegato.0.7.7a:

fixed a bug in bioLegatthat prevented canvas from appearing
fixed a bug that prevented sliders in menus from having negative values (Bugzilla# 1160)
fixed a bug that prevented bioLegatfrom reading some legacy .gde files. If the sequence contained newline characters, those were included in the sequence (Bugzilla# 1161)
fixed a bug in which pseudo-GenBank files generated by GDE were not read
fixed a bug which prevented the Documentation menu from being used. (Bugzilla# 1160)

version 2.8.6

fixed critical bug in bioLegato 0.7.7 which prevented menus from displaying properly

version 2.8.5

bioLegato has been upgraded to v0.7.7. This version introduces
the new table canvas, which is used by blmarker.
ribosome: new options for formating translated amino acid sequences
The following programs have been removed do to obsolescence:
- GDE (gde, mgde, tgde) - superseded by bioLegato programs bldna, blprotein, blmarker, bltree
- clustalw, clustalx - these are superseded by TCOFFEE
- Translate - superseded by ribosome

version 2.8

Getbirch - Getbirch is an automated install updater and installer, that supersedes these functions in birchconfig. Birchconfig is still used for adding local custom documentation and for uninstalling.
bioLegato has been reorganized into several new interfaces:
- birch - launcher for all GUI programs in BIRCH
- bldna - DNA/RNA sequence tasks
- blprotein - protein tasks
- blmarker - molecular markers
- bltree - phylogenetic trees
When upgrading from BIRCH 2.7 and earlier, local GDE menus items will be copied to corresponding directories in local/dat. It is important to do a manual check to see if menus have been added to the appropriate bioLegato interface.
Visualization of data in bioLegato now includes a variety of character color themes for proteins, nucleic acids, markers and phylogenetic trees.
During a new installation, birchhome.sh failed to change the userid of the BIRCH administrator in passwd.wrm, both for birchdb and lbirchdb. This prevented creation of a local birch database, meaning that documentation for locally-installed programs wouldn't appear in the database. This has been fixed.
A major reorganization of Python scripts has been done. This addresses future compatibility with Python 3, as well as creating sets of reusable classes that will simplify future development.
A number of the bioLegato scripts failed to clean up temporary files after execution was completed. These have been fixed.
The Phylip programs drawgram and drawtree require the libXaw.so.7 library, which is not found in some Linux distributions. This library has been added.
PostScript files on MacOSX. The utility script PStoPDFviewer.sh automatically runs ps2pdf to convert PostScript files to PDF. However, ps2pdf appears not to be part of the standard OSX install. PStoPDFviewer has been modified to directly open files using 'open', which knows how to automatically convert PostScript files. This problem prevented viewing of output from drawtree and drawgram.
Sequin has been upgraded to version 10.0.
Bluejay has been upgraded to version 1.3.
ACeDB is now considered a legacy application, and will be replaced with a different lightweight database system in a future release. This is partly because the code was compiled on a 32-bit Linux system in 2003 and is almost impossible to re-compile today. As a temporary fix, the scripts that launch xace or tace (birchdb, lbirchdb, l-gbirchdb and acedemo) have been upgraded to load 32-bit libraries included in lib-linux-intel or lib-linux-x86_64.
GDE has been frozen as a legacy application, and will no longer undergo development. The program will still work with all GDE menu files as of BIRCH 2.7, but future changes will only affect the biolegato family of programs. IN THE NEXT MAJOR RELEASE, GDE WILL BE DELETED FROM THE BIRCH SYSTEM.