BIRCH Version 3.90

NEW:

  • BioLegato 1.1.2
  • New platform: macos-arm64 (eg. M1, M2, Apple Silicon)
  • many updates to software packages
  • full Python3 compliance


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:


Current Stable Version 3.90 (December 31, 2023)

NEW  and Updated Software applications and features:

DELETED applications:
End of Life Platforms
RHEL 7 - Red Hat Enterprise Linux and related distributions will no longer be supported in future releases of BIRCH. Subsequent releases will be developed and tested on RHEL 8 or later.
Ubuntu 18 - Ubuntu LTS 18.0.4 LTS and related distributions will no longer be supported in future releases of BIRCH. Subsequent releases will be developed and tested on Ubuntu 20.0.4 LTS or later.

Python2 - BIRCH no longer requires python2. All python scripts now use python3.

Bug Fixes (See BIRCH Bugzilla at Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)



Version 3.87 (August 4, 2022)

NEW  and Updated Software applications and features:


DELETED applications:

Bug Fixes (See BIRCH Bugzilla at Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)




Version 3.86 (May 20, 2022)

NEW  and Updated Software applications and features:
DELETED applications:

Bug Fixes (See BIRCH Bugzilla at Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)

log4j2 - At present, it does not appear that any of the Java programs distributed with BIRCH presents vulnerabilities due to the log4j2 exploit.

We have confidence in this assertion for several reasons:
Out of an abundance of caution, further investigation into this potential problem are ongoing.

Version 3.85 (September 6, 2021)

NEW  and Updated Software applications and features:

This release introduces a new BIRCH home page that should be easier to navigate and customize, as well as being more aesthetically appealing than the prior home page. It is enough of an improvement that it's worth upgrading from 3.80.

Rather than having all main links displayed on the home page, links have been organized into a navigation bar with dropdown menus. This still allows the user to find what they want almost instantly, without the screen clutter of the previous version of the web site.

Local pages, such as instructions for connecting to a BIRCH server, or first time setup, are can be seamlessly integrated into the nav bar menus. This helps the new user see how to do things on their site.

Bug Fixes (See BIRCH Bugzilla at Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)





Version 3.80 (July 5, 2021)

NEW  and Updated Software applications and features:

DELETED applications:


Bug Fixes (See BIRCH Bugzilla at Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)




Version 3.71
(July 29, 2020) - Feature upgrade to 3.70


NEW  and Updated Software applications and features:

DELETED applications:


Bug Fixes (See BIRCH Bugzilla at Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)




Version 3.70
(July 22, 2020)


NEW  and Updated Software applications and features:
DELETED applications:

Bug Fixes (See BIRCH Bugzilla at Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)


Version 3.60 (April 24, 2020)

NEW  and Updated Software applications and features:


DELETED applications:

Bug Fixes (See BIRCH Bugzilla at Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)




Version 3.50
(June 20, 2019)


NEW  and Updated Software applications and features:

This release represents a massive addition to the BIRCH system, with complete sets of tools for genome and transcriptome assembly and gene expression data. Most of these capabilities are unified in a new BioLegato interface called blreads. Because most genome and transcriptome tasks work with numerous files, blreads presents the files as a spreadsheet (akin to a file manager) in which files can be selected as input for a wide variety of programs. Because these tasks are time-consuming, notification of completion by email is supported.

DELETED applications:

none

Bug Fixes (See BIRCH Bugzilla at Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)




Version 3.40 (May 2,2017)

NEW  and Updated Software applications and features:

DELETED applications:


Bug Fixes (See BIRCH Bugzilla at Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)




Version 3.30
(November 21,2016)


NEW  and Updated Software applications and features:



DELETED applications:



Bug Fixes (See BIRCH Bugzilla at Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)



version 3.20
(May 18,2016)


NEW  and Updated Software applications and features:


DELETED applications:



Bug Fixes (See BIRCH Bugzilla at Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)


version 3.15 (January 6,2016)

NEW  and Updated Software applications and features:


DELETED applications/features:


Bug Fixes (See BIRCH Bugzilla at Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)


version 3.10 (July 20,2015)

NEW  and Updated Software applications:


DELETED applications:


Bug Fixes (See BIRCH Bugzilla at Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)


version 3.00 (May 2,2015)

NEW  and Updated Software applications:

DELETED applications:


Bug Fixes (See BIRCH Bugzilla at Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)



version 2.96
(May 21, 2013)

NEW  and Updated Software applications:



DELETED applications:
Bug Fixes  


version 2.95 (September 24, 2012)

NEW  and Updated Software applications:
DELETED applications:
BIRCH     


version 2.9

version 2.8.6


version 2.8.5


version 2.8