CURRENT RELEASE

Version 2.7, May 20, 2010
--------------------------------

o BIRCH now supports MacOSX on x86_64 architecture. At present
  this is still a set of Unix programs that run on OSX. That is, 
  even GUI programs still need to be launched from the command line.
  Full integration with the Aqua desktop will appear in a future release.
o Biolegato 0.7.0
  o colour schemes (eg. hydrophobicity) for aminoacids or nucleotides
    can now be read from files
  o degap - removes gaps from multiple alignment
o When doing a new BIRCH install, a web browser with the BIRCH documentation
  home page will pop up when the install is complete. At this point,
  the user can add a bookmark making it easier to find the local copy of
  the documentation.
o Documentation has been added for setting up the local KDE desktop.
o New application: Seahawk - Seahawk takes just about any kind of
  textual data and discovers web services that will run with that data.  
o birchconfig now does a better job figuring out whether a Linux
  system is i686 or x86_64.
o birchconfig - corrected an error, which set the BIRCH home directory
  to the home directory of the user installing BIRCH, regardless of
  whether or not that was the directory in which BIRCH was being
  installed.  
o The installation instructions have been simplified
  substantially, and should be easier to follow.
o In previous releases, the file menulist was in the local/makemenus directory
  when it should have been in local/makemenus/menus. This has been
  fixed, and after updating, this file will appear in your already-existing
  local/makemenus/menus directory, if it was not already there. As well,
  Some README files have been added to local/makemenus directories,
  and some empty directories for each menu, just to remove one potential
  source of error when you go about adding locally-installed programs to
  biolegato, mbiolegato and tbiolegato. Any files that already exist
  in the local directory tree will NOT be overwritten!
o makemenus.py now allows comments in menulist files.
o primer3 has been updated to version 2.2.2
o NCBI Sequin has been upgraded to version 9.50.  
o Mesquite has been upgraded to version 2.72.
o TCOFFEE has been upgraded to version 8.14.
o The FASTA3 package has been upgraded to version 35-4.11. tfasta 
  is no longer distributed with this package. Use tfastx or tfasty.
o Jalview has been upgraded to version 2.4.0.b2.
o On some systems, the user's rc files (eg. $HOME/.bashrc) are
  created automatically with read-only permissions, which prevented
  the newuser script from setting up a user's account to use BIRCH.
  newuser now gives the user write and execute permissions, if these
  files exist. 



Version 2.6, March 2, 2010
-----------------------------------

o The current version of bioLegato is 0.6.2. This version includes
  major improvements in features and usability:
  o new right-click menus from within name pane and sequence pane
  o can change protections for characters in selected sequences in 
    one step
  o decreased memory footprint
  o Allows copying and pasting with system clipboard
  o more intuitive cursor movement within multiple alignments
  o multiple alignment canvas can now be split horizontally into
    two windows
  o now has a file chooser button in program menus. Previously,
  many programs required you to type in a file name when reading
  a file from a menu.
  o Now supports grouping of sequences, for simultaneous editing
    of multiple alignments
  o Now supports rectangular selection of blocks of subsequences from
    a multiple alignment
o On linux-intel, Sequin9.2 requires libXm3.so.3, which has been added
  to lib-linux-intel.
o Fixed a bug in whoami wrapper, which resulted in an infinite recursion
  on some systems.
o Added libncurses.so.5 to lib-linux-x86_64. This is required for
  xace, and is not always found on 64-bit linux systems.
o Added biolegato documentation to Documentation menu.

o htmldoc.py modified so that programs listed as being launchable
  from GDE are now also listed as being launchable from bioLegato.  
o bioLegato versions of all tutorials are now available.
o Fixed some broken links in tutorials


Version 2.5, September 20, 2009
-----------------------------------

***********************************************************************
bioLegato - This release includes the first public release of bioLegato, 
a Java replacement for GDE. The current release, Version 0.5.7, has 
almost all the functionality of GDE, and is now the preferred graphic
interface for BIRCH.
***********************************************************************

o Fixed a problem in which BIRCH installation would fail on systems where
  the whoami command is not found in a directory listed in the system $PATH.
o GDE has several issues on recent Linux releases that prevent it from running.
    * Fedora11 - xset/font problem - won't launch
    * Ubuntu 9.04 - launches, but entire X11 desktop freezes
o The 'vncsetup' script sets up a user's account to run
  vnc. The BIRCH Administrator can activate this feature by putting an
  'xstartup' file in $BIRCH/local/admin. vncsetup is run automatically
  from the 'newuser' script, so that all new users would automatically 
  have a working .vnc directory.  
o FASTA files produced by NCBI have definition lines in the form
  >gi|169079|gb|M18250.1|PEADRRB Pea (P.sativum) disease resistance
  whereas most FASTA files have a definition line like
  >PEADRRB - Pea (P.sativum) disease resistance
  Many programs cannot read the NCBI style, or truncate the lines at
  unpredictable places. ImportForeignFormat uses sed to to change the second
  pipe character to a blank so that the gi number is used as a name
  and the rest of the line is read as the definition.
  >gi|169079 |gb|M18250.1|PEADRRB Pea (P.sativum) disease resistance
  This way, at least we have the gi number, and know it is a gi number
  This should not affect any other files read by readseq, other than
  NCBI generated files. The bioLegato File-->Open function does not yet
  have this fix, so it won't properly read NCBI Fasta files.  
o Readseq has been upgraded to version 2.1.27. 
o Due to an increase in the size of Taverna by almost an order or magnitude,
  Taverna is no longer distributed with BIRCH. If you need Taverna you
  can install it in $BIRCH/local/java.
o Bluejay has been updated to the current version, Aug. 19, 2008.
o NCBI sequin has been updated to version 9.20.  
o Netblast (blastcl3) has been updated to version 2.2.20. This fixes 
  a problem that would sometimes cause output files to be truncated.
o An error was fixed in which URLs to local copies of documentation
  were incorrect when a new BIRCH installation was done in a directory
  other than the BIRCH home directory.
o On Linux, locations of BIRCH manual files were to the current list of
  directories found using man -w. This option for the man command is broken
  in some Debian releases. Now, for all platforms, BIRCH gets the current
  list of directories from $MANPATH.


Version 2.45, April 6, 2009
-----------------------------------
o DIALIGN-TX - Dialign is a multiple sequence alignment program that is often
  a good alternative to Clustal and TCOFFEE. It is avilable at the command
  line and in GDE Alignment menu.
o FEATURES - A bug has been fixed which caused features to execute getob
  in an infinite loop, for cases in which FEATURES read an empty GenBank
  file.
o Extract subset - It is now possible to automatically extract subsets
  of the sequences in a GDE window using Edit --> Extract subset. Given a
  list of names to extract, Extract subset will open a new GDE window
  containing only those sequences in the list.
o Sequin has been updated to Version 8.10 for solaris-sparc, solaris-amd64.
o Taverna has been upgraded to version 1.7.l. At this time the PDF
  manual for 1.7.1 was not available, so the PDF for 1.6.2 has been
  retained. HTML documentation is current for version 1.7.1.
o dGDE is unavailable in the current release of BIRCH.
  dgde relied upon the now defunct SeqHound data warehouse
  to retrieve data. New middleware is being written for dgde
  that will utilize the NCBI EUtils web services.
  A working version of dgde using EUtils will appear in
  a future BIRCH release.



Version 2.4 May 27, 2008
---------------------------------------------
o GDE launches text editors to display program output, which can create sevaral
  problems. First on some Linux systems, setting LD_LIBRARY_PATH in gde, dgde, mgde and tgde
  cause nedit to crash if used as the GDE text editor, as specified in
  $GDE_TEXTEDIT. Secondly, some editors such as gedit will, by default, open all files
  as tabs in a single window. It is better to open each file in a separate window, because
  that makes it more obvious to the user that there are several files. For several editors,
  wrapper scripts have been created which fix these problems. GDE and the scripts
  that it uses for displaying output now call a script called choose_edit_wrapper.sh, which
  sets GDE_TEXTEDIT variable to the name of the appropriate wrapper eg. nedit_wrapper.sh,
  gedit_wrapper.sh. The following scripts have been modified to fix this problem:
  dgde, gde, mgde, tgde, gde.treeoutput.csh, gde_help_viewer.csh, primer3run.csh,
  fastaout.csh, dbsout.py.
o The LD_LIBRARY_PATH is no longer set globally. Rather, any application
  that needs non-standard libraries must set this variable in a
  wrapper script.
o Bluejay has been updated to Version 1.0, April 25, 2008
  This fixes a problem with finding BioMOBY web services, which
  was broken in a previous version.
o The fasta package has now been upgraded to version 3.5 with the 
  following important changes:
  - new programs: GGSEARCH,GLSEARCH
  - deleted programs: PRSS, LFASTA
  - updated LALIGN, SSEARCH
  - better statistics
  - more uniform command line options
  - Due to problems compiling the tfasta35, tfasta34 has not been replaced.
o mGDE can now directly import .csv files of molecular markers which have
  been generated by spreadsheets. In mGDE use 'File --> Import Discrete
  Data from CSV file'.
o The FTP directory organization for Bill Pearson's fasta2 package has changed.
  fasta2install.sh has been updated to find the programs at their new location.
o To enhance the readability of install messages, birchconfig now puts
  separator lines between sections of messages written to
  birchconfig.screen.
o The wrapper scripts dgde, gde, mgde and tgde have been rewritten as
  sh scripts.
o The following csh scripts have been rewritten as sh scripts, and the
  file extensions changed to .sh: newuser,
  nobirch, birchhome.csh, makelinks.csh, fasta2install.csh,
  fasta3install.csh, doc2ace.csh, dat2ace.csh, tbirchdb.csh, PStoPDFviewer.csh.
o On some systems, setplatform.csh could not overwrite default
  copies of local.profile.source and local.source, which resulted
  in binaries and scripts not getting into the $PATH. This script
  has been replaced with setplatform.sh, which unsets 'noclobber',
  ensuring that files can be overwritten. This problem only affects
  new installations, and has no effect on upgrades.
o On some systems, python is not present in the C-shell $path.
  The installation script runmakemenus.csh, which calls python,
  has therefore been replaced with runmakemenus.sh.

Version 2.35 February 25, 2008
---------------------------------------------
o Changes to libraries in Fedora 8 Linux prevented dgde, gde, mgde, tgde
  and TREETOOL from running, giving the following message:
  
  gde.bin: xcb_io.c:285: _XAllocID: Assertion `!(dpy->flags & (1L << 3))' failed.
  Abort
  
  The original libraries from Fedora 4 have been added to $birch/local/lib-linux-intel
  to allow for backward compatibility.
o The script PStoPDFviewer.csh has been added for systems on which 
  no PostScript viewer is available. This script converts the PostScript
  file into a PDF file, and then opens the default PDF viewer. PStoPDFviewer
  can be set as the default PostScript viewer in local.cshrc.source and 
  local.profile.source.
o Some Linux distributions do not include lucida B&H fonts needed by GDE
  and Treetool. These fonts have been added to binaries for linux-intel and 
  linux-x86_64. Solaris systems should already have these fonts.
o local.profile.source now sets the command prompt for zsh.


Version 2.3 November 26, 2007
---------------------------------------------

 o Sequin has been upgraded to the most recent release. 
 o A link for the Release Notes has been added to the Home page.
 o Taverna has been upgraded to version 1.6.2.
 o Bluejay has been upgraded to the Oct. 11 2007 version.
 o The fasta ftp site has been discontinued. Installation scripts
   now download fasta programs from ftp.ebi.ac.uk.
 o Support for linux-x86_64 is currently under development. At present,
   most of the programs have been recompiled as native 64-bit binaries, 
   but some are still the original 32-bit binaries. However, linux-x86_64
   runs 32-bit binaries very well.
 o The fasta programs are downloaded by FTP and compiled as part of each
   install. On some systems, the firewall will cause FTP downloads to fail
   unless they are done in the passive mode. There is no command syntax that
   is consistent for all Unix systems for passive FTP. Therefore, the install
   scripts in install-birch/fasta have been modified to choose pftp or ftp -p,
   if pftp is not available.
 o On Ubuntu, Taverna could not run dot, because libpng.so.2 was missing.
   This file has been added to lib-linux-intel. 
 

Version 2.2 May 17, 2007
---------------------------------------------

 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 

Version 2.1
---------------------------------------------
December 15, 2007

 o With Fedora 5 and later, the syntax for the tail command is no longer
   consistent between Unix and Linux. Fedora uses 'tail -n number', while other
   Unix/Linux versions use 'tail +number'. There is no syntax that works
   for both. Scripts for the following programs
   have been revised to work around this problem: numseq, dxhom, pxhom,
   discrete data distance methods, fastDNAml, align, primer3 and testcode. 
 o Numerous improvements have been made in birchconfig.java and installation
   scripts to detect errors during installation and updating.
 o On systems where users have limited disk quotas, core dumps can
 sometimes cause users to exceed their quotas. BIRCH now uses limit (C-shells)
 and ulimit (BOURNE shells) to limit the size of core files to 0.
 If necessary, this could be overridden in local.cshrc.source and
 local.profile.source.

Version 2.0
---------------------------------------------
October 1, 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 (update-local.sh) to the update procedure used
  by birchconfig.java. 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.


A1.99
---------------------------------------------
June 27, 2006

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
  page.
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.


A1.98
---------------------------------------------
April 13, 2006

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.



A1.97
---------------------------------------------
January 28, 2006

o The programs called by GDE have been redistributed
  among four specialized interfaces:

    * GDE - sequence data
    * dGDE - list data
    * mGDE - discrete state data
    * tGDE - phylogenetic tree data

In particular, tree drawing programs (Drawtree, Drawgram, Treetool, ATV)
have been moved from GDE to tGDE, and phylogeny programs for discrete 
state data (RESTML, DiscDist and DiscPars) have been moved to mGDE.


A1.96
----------------------------
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 birchconfig.sh. 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. birchconfig.sh 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 UNINSTALL-birch.sh


A1.95
----------------------------
Oct. 23, 2005
o On some systems, the birchdb, lbirchdb and l-gbirchdb couldn't find
  file viewer programs. Symbolic links were added from $BIRCH/script
  to correct this problem.
o Fixed a bug in htmldoc.py that caused it to crash when a File: object
  had no document URL.
o The Taverna Workbench has been upgraded to version 1.3.
o A versioning system has been added. When a BIRCH release is built, the 
  current version designation is written to doc/BIRCH.version, and the
  date and time are written to doc/BIRCH.version.timestamp. The version
  designation is also written to birchconfig.screen during installation.
o The ACEDB programs xace and tace have been upgraded to version 4.9.27.
  On Solaris, a number of gnome libraries are needed which may not be
  installed on all systems. They have been added to lib-solaris-sparc.
  Programs that rely on xace or tace (acedemo, birchdb, lbirchdb, l-gbirchdb,
  tace.csh)have lib-solaris-sparc added to the LD_LIBRARY_PATH.
o Fixed an error in profile.source that prevented binaries in 
  local/bin-solaris-sparc or local/bin-linux-intel from being found.
  This error only affected users using Bourne-type shells (eg. sh, bash
  ksh, ash) and did not affect csh or tcsh users.
o The environment variable BIRCH_LOGGING has been added. If BIRCH_LOGGING=1,
  messages are written to local/admin/logins.log when a user logs in,
  and to gde.log when a user launches GDE. By default, BIRCH_LOGGING=0,
  in case BIRCH has been installed in a read-only filesystem. (Otherwise,
  login scripts and GDE would fail). To turn
  on logging in a read-write filesystem, the sysadmin must set 
  BIRCH_LOGGING=1 in local.cshrc.source and local.profile.source. 
  A documentation page has also been added for logging usage.
o Added user FAQ and BIRCH administration FAQ.
o Fixed bug in birchhome.csh that looked for BIRCH homedirectory
  by searching for 'homedir' in BIRCH.properties. It should have
  been looking for BirchProps.homedir. This would cause birchhome.csh,
  and thus, all installation steps, to fail on systems upgrading
  from the most recent development versions, because birchhome.csh
  would also find the string birchhomedir, which would mess up the
  $BIRCH enviroment variable.
o birchconfig has a new method that guides the BIRCH administrator 
  locate the correct URLs for the local BIRCH site, and then to set these
  URLs in the BIRCH documentation. In the main birchconfig window, press
  "Set Web location for documentation."
o On BIRCH Home page, the "Your Unix Desktop" section now has links
  for both "First time setup" and "User's Guide", for each desktop.
  Depending on what is available on your system, you can add a number
  of different desktops to this section. Sample HTML is available in
  local-generic/public_html/localdesktop.html.
o GDE has been upgraded to macgde.1.9.5.


A1.91
----------------------------
Aug 5, 2005

o A minor bug in dGDE, which prevented it from finding the openwin
  libraries, has been fixed.
o The binaries files now include libraries as well. For example, on a Solaris
  system, the file bin-solaris-sparc_A1.9.tar.gz contains the directories
  bin-solaris-sparc and lib-solaris-sparc.
o Deleted a duplicate line from the May 7 version of browser.csh that 
  prevented the program from working.
o Updated BIRCH Administrator's Guide to cover installation using the
  install wizard.
o An install wizard is now available. This graphic installer can do a
  new install, uninstall, and update an existing BIRCH site to a new version.
  cd to install-birch and type './birchconfig.csh'.
  
A1.8
----------------------------
May  13, 2005

o Two new parts of the BIRCH home page can be now customized for your
  local BIRCH site. The files localdesktop.html and localapps.html 
  specify links to documentation for various desktops installed on
  your system (eg. Sun Java Desktop) and to lists of applications
  on your system (eg. office software)
  
o The BIRCH_PLATFORM environment variable, which is set in local/platform.source
  and local/platform.profile.source, should be set to "solaris-sparc" on systems
  running Solaris on the Sparc architecture. The old value of "sun" is
  deprecated, and support for "sun" will be removed in a future release.

o GDE 2.4 is an update of GDE 2.2 by Eric Linton from Michigan State
  University. Fixes include: Linux version now correctly reads
  GenBank files with circular sequences; GDE no longer crashes
  when cutting blocks of an alignment, or trying
  to cut when permissions do not allow cutting
  
o Added E-value option to FASTA menus

o NEW: Bluejay genome viewer and annotator (http://bluejay.ucalgary.ca)

A1.7
----------------------------
March 17, 2005

o Readseq upgraded to version 2.1.21.

o Mesquite upgraded to version 1.05.

o NEW: Taverna Workflow Designer. Taverna is a graphic workbench
for designing automated workflows using hundreds of biological
web services.

March 6, 2005
dGDE - SeqHound 2.5 method SHoundFindAccList doesn't handle Accession
numbers with the version field eg. AB005321.1. As a temporary fix,
the Convert Name/Acc to GI menu item will truncate the version 
field. The most recent SeqHound does correctly handle the version
field, so this fix should be removed when Leash is updated to the
most recent SeqHound. 

March 5, 2005
The script browser.csh is used to launch a browser from any application.
When configuring an application to run a browser (eg. for reading
documentation) it should launch browser.csh, rather than specifying
a specific browser. browser.csh runs the browser specified in the
environment varialbe BIRCH_NETSCAPE. For older browsers (eg. Netscape 7.1)
it browser.csh also detects whether the browser is already running,
and if so, launches a new window using the '-remote openURL' option. 

Feb. 28, 2005
Scoring matrix files for fasta2 programs were moved to a separate
directory, $dat/fasta2. This is because the fasta2 programs
can only read files using a half-matrix format, whereas programs
in fasta3 can only read full-matrix foramt.

Feb. 18, 2005
The tutorials directories were reorganized. $BIRCH/public_html/GDE/tutorials
has been replaced by public_html/tutorials/GDE/.
As well, the symbolic link $birch/tutorials, which previously pointed
to public_html/GDE now points to public_html/tutorials.
A temporary symbolic link public_html/GDE --> tutorials/GDE
has been added. I think I already have changed all pages, both
on the BIRCH web site and on pages belonging to 'frist', but
we'll leave this link for awhile.

Feg. 15, 2005
A major reorganization of BIRCH documentation has done. Documentation
is now maintained in two databases, one for the BIRCH distribution,
and one for locally-installed programs. The script htmldoc.py reads
both databases and generates a unified set of web pages, listing 
programs by category, by package, and an alphabetical program index. 
The user sees a single view of all documentation. The BIRCH installation 
and updating pages have been revised to include running htmldoc.py. Further 
documentation still needs to be written to describe the process of adding 
locally-installed documentation to the database.

Feb. 3, 2005
A bug in the Phylip RESTML program causes RESTML to hang when
the "Speedier but rougher analysis" option is used. This option
has been removed from the GDE menu for RESTML until RESTML is
fixed.

Feb. 1, 2005
FASTA package - Bill Pearson's Makefile.sun defaults to use the
Sun cc compiler, which is often not available on many Solaris systems.
Therefore, by default, the fasta install scripts use gcc, and to do this
the scripts will replace 'cc' in Makefie.sun with a call to gcc, using
appropriate switches. BIRCH admins who which to use the Sun cc compiler
can run the install scripts using the -S option.

A1.6
-----------------------
January 30, 2005

January 28, 2005
Fixed a bug in FEATURES, which attempted to retrieve
entries needed to resolve feature expressions from SeqHound,
during the first pass. This only caused problems when 
the host had no Internet connection. 

January 27, 2005
Phylip has been upgraded to v3.63. This upgrade vastly expands
the number of programs and features available for running PHYLIP
through GDE. The only thing that still needs updating are the 
GDE tutorials for phylogeny.

January 23, 2005
The Linux-Intel version of GDE crashes if an "out" file is
declared in the menu item, but "out" does not exist. This
problem has been corrected for DNA/RNA-->Ribosome, and for
many of the menu items in dGDE.

January 9, 2004
NCBI Sequin has been upgraded to version 5.35. This fixes a serious
font problem that affected the Linux/Intel version of the program,
in which windows that should have text would appear blank.

January 8, 2004
The files local.cshrc.source and local.profile.source have been updated to
include Mozilla Firefox as a supported browser, for use by
GDE.


A1.5
-----------------------
December 7, 2004

o Enhanced customization of BIRCH homepage. customdoc.py was modified 
to allow sections of the home page to be replaced with local HTML,
each time the BIRCH system is updated.

November 15, 2004

o Moved $BIRCH/local/script and $BIRCH/local/bin-xxx-xxx to beginning
of $path, so that locally-installed progrmas can override system
default copies of a program, by putting them into local directories. 

o makemenus.py: Modified makemenus.py to work with older versions of 
python, which would not read $dat/GDE/makemenus/ldir.param correctly.
This would cause local GDE menu items to be omitted when runing makemenus.py.

August 23, 2004
The lines

# Print login messages
cat $BIRCH/local/admin/Login_Message

have been moved from admin/login.source to local/admin/local.cshrc.source,
and from admin/profile.source to local/admin/local.profile.source. If you
are updating from BIRCH version A1.4 or earlier, you should manually
insert these lines into local/admin/local.cshrc.source and
local/admin/local.profile.source.

August 19, 2004
makemenus.py has been simplified so that it always runs 
from with the directory containing makemenus files.
The previous version used the BIRCH environment variable
to set paths, which was problematic for creating 
.GDEmenus files for applications other than BIRCH.


A1.4
-----------------------
July 19, 2004

o Revised BIRCH Administrator's Guide to clarify the point that 
there should be a separate user account for the BIRCH Administrator.
Also moved instructions on running 'newuser' from 
$birch/local/public_html/setup/setup.html
to $birch/public_html/newuser.

o In some cases, bash was not setting $BIRCH and other environment 
variables. Modified newuser and nobirch scripts to, respectively, 
add and delete source lines to .bashrc

July 15, 2004

o Database search: New GDE menus have been added that perform BLAST
searches remotely at NCBI, returning the results when ready.
By default, FASTA only searches user-created databases. 
It is also possible to install local BLAST databases and
programs. GDE menuitems
for searches of locally-installed database are found in
$birch/local/dat/GDE/makemenus/menus. These can be locally modified, 
and used to replace the default menu items. 

July 14, 2004

o Some housecleaning and reorganization has been done to eliminate
programs that don't work or are obsolete from BIRCH, and to
re-organize documentation web pages into standard and local
sections.

July 12, 2004

o The current Linux binaries of ENTREZ, SEQUIN and CLUSTALX
may not work on all systems, due to differences in Motif
libraries from system to system. This problem is currently
under investigation.

Version
A1.3
-----------------------
May 16, 2004
o Added TCOFFEE - multiple sequence alignment program. TCOFFEE can
be fun from the command line and from GDE.

January 20, 2004
o The ACeDB demo has been updated to work with more recent
versions of xace.

December 6, 2003

o NUMSEQ and RIBOSOME can now use all genetic codes from NCBI.
In GDE, translations generated by RIBOSOME can be sent to a new
GDE window.

Version
A1.2
----------------------- 
November 29, 2003

o Improved tutorial on creating large sequence datasets. 

November 25, 2003

o Added -z parameter, which chooses statistical scoring model, to
GDE menus for FASTA programs. In particular, -z 11 -15 are needed
to generate realistic E values when searching a very small dataset.
In this case, scores will be compared to scores for randomly-shuffled
sequences, as in PRSS.


November 16, 2003 

o Updates to FEATURES and GETOB. Added feature keys: operon, oriT,
primer and snoRNA. Updated GETOB to handle feature locations
with references of the form ACCESSION.VERSION:<location>

July 7, 2003

o Added admin.uninstall directory. If BIRCH is to be permanently
deleted from a system, rename it as admin. This directory contains
dummy cshrc.source and profile.source files that run the next
time each user logs in. Theses files act like the nobirch script,
deleting BIRCH setup lines from .cshrc, .login etc.



Version
A1.1
-----------------------
July 5, 2003

mrtrans has been modified to allow names longer than 9 characters.
As well, a new mrtrans menu makes sure that lowercase amino acids
are changed to uppercase, which is required by mrtrans.

June 21, 2003 

Automated deletion of BIRCH access for a user account is now possible
by running $BIRCH/admin/nobirch.

June 18, 2003

Discovered that bash will only execute the first of ~/.bash_profile,
~/.bash_login or ~/.profile. On systems in which bash is the
default, .profile would never be executed, so $BIRCH/admin/profile.source
would never be executed. Modified the newuser script to add
add_to_profile to .bash_login and .bash_profile.

Version A1.0
----------------------------
June 2, 2003

The .GDEmenus file for FEATURES has been modified for better
compatibility with the most recent release of readseq.

May 28, 2003

source and '.' lines added to users' .cshrc, .login and .profile
files now include an if statement checking for the existence
of the source file before executing. This prevents an error
message in case BIRCH is uninstalled.

FEATURES was changed to use 'nice -n x' which is allowed by 
both csh and tcsh.

miniBIRCH is a small set of BIRCH files which must be 
customized locally at each BIRCH site. In a workshop,
where a full BIRCH implementation exists on the server,
each student installs miniBIRCH and then runs 'makelinks.csh'
to create symbolic links to the other BIRCH directories.
In effect, each student has his/her own BIRCH site.

The BIRCH installation pages were reorganized such that
each task in installation is now on a separate page. 
New installations, miniBIRCH installations, and
updates all use slightly different steps but share
most steps in commmon. Thus, there are separate 
checklists for each type of installation, all referencing
most of the same pages.

May 21, 2003

Minor fix to fastaout.csh to eliminate lines from namefile
beginning with '>>' or '#'

May 19, 2003
makemenus.py has been modified so that a locally-modified
GDE menu item will replace the menu item supplied with
BIRCH.

Version A0.04
---------------------------------

May 14, 2003

Updated documentation on setting up the CDE desktop to include
screen shots of most important Style Manager menus and 
more complete descriptions.

April 25, 2003

Generalized makemenus.py to work independently, if GDE
is not being used as part of a BIRCH implementation.


April 16, 2003

cshrc.source, profile.source - Moved PATH and MANPATH settings
out of login.source and profile.login.source. Some installations
do not use .login files, so these critical variables would
never get set. Because we can't count on .login being used,
it is best to keep things in cshrc.source and profile.source
unless it absolutely positively must be done only at login time.

April 2, 2003

GDE
---
A new mechanism has been designed for managing and updating .GDEmenus.
The individual menu items have been broken up into separate 
.item files, which are organized into separate directories named
after the names of the menus in which they appear. Changing menu
items now requires 2 steps: 1) modify or add a .item file
2) Run makemenus.py to recreate the new .GDEmenus file by concatenating
the .item files.

This method makes it easier to create any number of .GDEmenus files
customized for each platform. In particular, since some programs
are present on one platform but not another, each .GDEmenus file
contains only the programs available on that platform. Currently,
there are separate GDEHELP directories (which contain .GDEmenus)
for Solaris-Sparc and Linux-Intel. cshrc.source and profile.source
have been modified so that the $GDE_HELP_DIR variable points
to the correct GDEHELP directory at login time.

Finally, these changes make it straightforward for local BIRCH
implementations to automatically add programs to GDE that are
not part of the official BIRCH distribution.

Early alpha releases
--------------------------------------

Mar. 11, 2003 
Installed Artemis v5.

   
Mar. 5, 2003

Installed tacg3.6b. This adds many functions for restriction
searching, including PDF maps and open reading frame display
along with sites, and search for matrix patterns.
Search for rules and regular expressions does not yet work.
TACG can be run from GDE or at the command line.

The GDE implementation calls $birch/script/browser.sh
to launch Netscape for displaying HTML output from the program.
In the future, browser.sh will be used for displaying 
HTML files from many applications.

Feb. 17, 2003

Completed getting Phylip programs to work under GDE in Linux.
This included 
   - adding the $RM_CMD command to scripts.
   - recompiling restml using maxsites=50
   - some corrections to fastDNAmlrun and dnaml.csh that
   were not working properly

Feb. 15

Downloaded pre-compiled treetool 2.0.2 for Linux
