Version 3.10 July 20, 2015 --------------------------------- NEW features and updates: - - - - - - - - - - - - - - - - - - - - o Artemis - The Artemis sequence viewer/annotator has been updated to version 16.0.0. It is now possible to retrieve sequences from NCBI directly to Artemis, and to export sequences from bldna to Artemis. o Default Helper applications (eg. text editors, web browsers) used by BioLegato can now be set in the BIRCH Administration Tool (birchadmin). The old GDE environment variables (eg. GDE_TEXTEDIT), previously set in $BIRCH/local/admin are no longer used. o Some BIRCH environment variables that goven how BIRCH behaves can be set in the BIRCH Administration Tool (birchadmin). These variables are no longer set in $BIRCH/local/admin. If you are upgrading from BIRCH 3.0 or earlier, they can be deleted from local.profile.source and local.cshrc.source. These include: o all GDE variables o BIRCH_TMP o BIRCH_LOGGING o BIRCHJAVACMD o BIRCH_NETSCAPE o BROWSER_OPENURL o lines setting the shell prompt o The BIRCH update/install wizard, getbirch, can now be launched from birchadmin. o Substantial updating of documentation for BIRCH system adminstration. o First time setup documentation has been added for the MacOSX desktop. DELETED applications: - - - - - - - - - - - Bug fixes: (See BIRCH Bugzilla at http://www.bioinformatics.org/bugs/?group_id=543) ------------------------------- o Note: Weblogo requires the Python numpy library, which is not distributed withe BIRCH. o Bugzilla #1202 - update_local.py fails to copy files to $BIRCH/local Version 3.00 May 2, 2015 --------------------------------- NEW features and updates: - - - - - - - - - - - - - - - - - - - - o BioLegato for NCBI Entrez - Three new BioLegato interfaces have been created. - blncbi: lets users construct Entrez queries to NCBI and returns results in in spreadsheet form, for subsequent retrieval. - blnfetch: retreives nucleotide sequences from remote BLAST or local FASTA searches. - blpfetch: retreives amino acid sequences from remote BLAST or local FASTA searches. The middleware for these BioLegato interfaces consists of two Python scripts, ncbiquery.py and seqfetch.py that can also be used at the command line. These scripts utilize the BioPython Bio::Entrez API. o BioPython 1.65 is now distributed as part of BIRCH, in the $BIRCH/python directory. o WebLogo 3.4 - Create sequence logos from multiple DNA or protein alighments o BioLegato 1.0.2 - - Export Foreign Format (bldna,blprotein,blnalign,blpalign) - Now has an option to export to a text editor. This is very useful if you want to copy sequences from BioLegato to paste into a web form. All formats supported by READSEQ are available. - blnfetch, blpfetch - new BioLegato interfaces that use the NCBI Entrez utilities to retrieve DNA, RNA or amino acid sequences from NCBI. bldna and blprotein will send GI or ACCESSION numbers from BLAST hits directly to blnfetch or blpfetch for easy retrieval of sequences. - bldna - GFETCH - retrieve sequences from NCBI using GI or ACCESSION numbers. - PCD has a new type called "textarea" that creates a text box in a menu. Any text can be pasted into the text box, such as lists of GID numbers or sequences. - pcdedit - graphical editor for PCD menus. Still considered an experimental program. - BioLego sequence canvas can split horizontally, allowing one to scroll horizontally through two parts of a DNA or protein alignment simultaneously. o BIRCH installation - - As a milestone toward making BIRCH completely platform independent the install scripts have been entirely re-written in Python. The shell scripts in install-birch are no longer distributed, and are replaced by Python scripts in install-scripts. o NCBI Sequin - Updated to Version 13.70 on linux-x86_64 and MacOSX. NCBI appears to no longer be supporting Solaris or 32-bit Linux. Consequently, the solaris-sparc, solaris-amd64 and linux-intel binaries have been updated to Version 13.05, the latest version for these platforms. DELETED applications: - - - - - - - - - - - o Bluejay, Seahawk, generic_ncbi_data_fetcher.pl Bug fixes: (See BIRCH Bugzilla at http://www.bioinformatics.org/bugs/?group_id=543) ------------------------------- o Bugzilla #1141 - In some installs, the code from htmldoc.py that generated web pages that indexed programs would fail, resulting in blank web pages. o Linux: added new libXrender.so and libXfixes.so libraries to bin-linux-x86_64 for compatabilty of xace with new linux releases. o Bugzilla #1182 - BIRCH installer now compares date of currently installed version to prevent installing an older version over a newer version. o Bugzilla #1183 - Edit --> copy should use FASTA format. Solved by adding Export Foreign Format to send output to a text editor. o Bugzilla #1184 - GetBirch failed to run update-local.sh. The latter has been replaced with a Python script, update-local.py, which is run by GetBirch. o Bugzilla bug #1185 -Need more robust way to recover if BIRCH download fails Several improvements so that BIRCH only needs a good $BIRCH/local directory for an update to be successful. o Bugzilla #1186 - Does UNINSTALL-birch.py need to run nobirch.py? o Bugzilla #1188 - SaveAs ignores selection and saves all sequences. o Bugzilla # 1190 - BioLegato failed to read GenBank entries containing the CONTIG keyword. Fixed, so that now BioLegato will create 0-length sequence when reading CONTIG entries. A more sophisticated fix would be to retrieve the complete CONTIG from NCBI, but because these are often in the hundreds of millions of nucleotides, for now we won't go that route. o Bugzilla #1197 - temp files deleted before chooseviewer.py can open them o Bugzilla #1198 - BioLegato can't delete characters unless sequence is in a group o Bugzilla #1199 - Cut and paste in a multiple alignment deletes gaps Version 2.96 May 19, 2013 --------------------------------- NEW features and updates: - - - - - - - - - - - - - - - - - - - - o 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 phylogenitic analysis or alignment display. By makeing 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. o Local BIRCH web site now displays current release number and timestamp. o BioLegato.0.7.9 o 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. o numerous bug fixes and performance enhancements including: o ability to set the text in the BioLegato window header bar o ability to specify order of items in a PCD menu o fixes to table canvas selection o fixes to PCD's platform specificity options o import column headers from file in table canvas o better ability to skip improperly constructed PCD menus o the BIRCH Launcher and birchadmin tool now have a launcher for Release Notes. o The BLAST+ programs from NCBI replace blastcl3 (netblast). New menus in bldna and blprotein expand the number of search parameters that can be set. o 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. o Calculation of protein statistics such as molecular weight and amino acid frequencies is done by a new program gstat.py, launched from blprotein. o 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: - - - - - - - - - - - o NCBI blastcl3 (netblast) o prostat and dbstat have been replaced by gstat.py (see above) Bug fixes: ------------------------------- o 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) o 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: - - - - - - - - - - - - - - - - - - - - o Cytoscape v2.8.3 - Visualize biochemical pathways o NCBI BLAST+ v2.2.26 - blastp,blastn, blastx, tblastn, tblastx, blast_formatter. DELETED applications: - - - - - - - - - - - o TM4 MIDAS BIRCH - - - - o In this version of BIRCH, all BioLegato menus have been translated into a new menu language called PCD. PCD 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 PCD. All future development of local menus should be done using PCD. o 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. o 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. o BIRCH launcher: The DNA, protein, and Multiple alignment menus have been merged into a single menu called "Sequence". o When launching bldna, blprotein, blmarker or bltree from the BIRCH launcher, the user is prompted to choose a working folder. o BioLegato - tool tips and icons have been added to most menus in BioLegato o BioLegato - it is now possible to set the title to appear at the top of a BioLegato window. Version 2.91, June 17, 2012 --------------------------------- o In recent versions of BIRCH, typing the single letter 'q' at the command prompt caused ALL programs in the script directory to be launched in succession. Apparently, a file named 'q' was accidentally made, containing a list of files in the script directory. This file also had the execute permission set, meaning that it could be executed as a script itself. q has been deleted from the script directory, eliminating the problem. Version 2.9, April 23, 2012 --------------------------------- o fixed a bug in the script that runs mrtrans that prevented mrtrans from running on some OSX systems. o 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) o The Phylip package has been upgraded to version 3.69. o 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. o 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) o bioLegato.0.7.7a: o fixed a bug in bioLegato that prevented canvas from appearing o fixed a bug that prevented sliders in menus from having negative values (Bugzilla# 1160) o fixed a bug that prevented bioLegato from reading some legacy .gde files. If the sequence contained newline characters, those were included in the sequence (Bugzilla# 1161) o fixed a bug in which pseudo-GenBank files generated by GDE were not read o fixed a bug which prevented the Documentation menu from being used. (Bugzilla# 1160) Version 2.8.6, September 29, 2011 --------------------------------- o fixed a bug in bioLegato that lost text boxes from menus, the second time a menu was used Version 2.8.5, September 26, 2011 --------------------------------- o New: MacOSX instructions for running VNC sessions o bioLegato has been upgraded to v0.7.7. This version introduces the new table canvas, which is used by blmarker. o ribosome: new options for formating translated amino acid sequences o The following programs have been removed due 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, April 12, 2011 -------------------------------- o 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. o bioLegato has been reorganized into several new interfaces: o birch - launcher for all GUI programs in BIRCH o bldna - DNA/RNA sequence tasks o blprotein - protein tasks o blmarker - molecular markers o 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. o Visualization of data in bioLegato now includes a variety of character color themes for proteins, nucleic acids, markers and phylogenetic trees. o 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. o 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. o A number of the bioLegato scripts failed to clean up temporary files after execution was completed. These have been fixed. o 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. o 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. o Sequin has been upgraded to version 10.0. o Bluejay has been upgraded to version 1.3. o 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. o 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 A FUTURE RELEASE, GDE WILL BE DELETED FROM THE BIRCH SYSTEM. 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: 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