BIRCH: Comprehensive bioinfo. system - Summary

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BIRCH bundles together many of the most commonly-used bioinformatics programs, unified through a graphic interface. BIRCH is designed to simplify the task of managing a bioinformatics core facility, but can also run on a single PC.

License: GNU Lesser Public License

Public areas This project has many places for you to explore and participate. The icons displayed below are also available at the top of the page for easy navigation.  Project homepage This home page points to the official page for this project, which may or may not be hosted at Bioinformatics.org.  Public forums There are 3 messages in 2 forums.  Project manager There are 0 open, public tasks, 0 total.  Support tickets There are 23 open tickets, 98 total.  Mailing lists There are 0 public mailing lists.  Public surveys There are 0 active surveys. SCM repository The SCM repository is a place for this project to store its source code. Members have access to change this master repository, while anonymous users may browse the most recent development version of this project. Instructions Download directory Projects may choose to have files other than their main releases available via this directory.

Members Project admins: Brian Fristensky Members: 3 [View all members] Downloads Module name: birch No releases [View all files] Latest announcements Submit Archive Subscribe BIRCH Version 2.0 Submitted by Brian Fristensky; posted on Thursday, October 05, 2006 o Some Linux distributions (eg. Fedora) do not have Java, but rather, a GNU bytecode interpreter called gij. gij did not work correctly with ANY Java application tested. The solution is to install the real Java from Sun, and make sure that java (and not gij) is in the $PATH. Instructions for this workaround have been added to the Pre-installation instructions. o Fixed some problems with fasta2install.csh and fasta3install.csh. On some systems, these scripts did not correctly detect the available C-compilers. o A major re-organization and rewrite has been done for documentation linked from the BIRCH home page under the name "Using Unix from Anywhere". The new documentation goes into more depth on using commandline clients, VNC, X-terminals, and other thin clients. o The re-organization of documentation has prompted the addition of a new script (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. BIRCH Version A1.99 Submitted by Brian Fristensky; posted on Wednesday, June 28, 2006 BIRCH Version A1.99 o miniBIRCH is now supported by birchconfig, the graphic install wizard. The install procedure for minibirch is almost identical to that for a complete BIRCH installation, with the addition that for miniBIRCH, the New Install window will have an additional 'miniBIRCH Master Directory' field. o New: ArrayNorm - Normalize raw gene array data, prior to analysis o New: TIGR-TM4 Microarray programs: ExpressConverter - converts array data to TIGR format MIDAS - Normalization and analysis MEV - Multi-experiment viewer for data mining o New: weighbor: Neighbor-Joining program which produces more reliable trees than traditional NJ. Available as an option in GDE. o Documentation pages for Packages and Programs now contain links to a glossary page which gives definitions for each field on the 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. ======================================================== The latest release of BIRCH (A1.99) is available at the BIRCH Web site http://home.cc.umanitoba.ca/~psgendb under the link 'BIRCH Administrator's Guide'. BIRCH A1.98 - updates and new features Submitted by Brian Fristensky; posted on Monday, April 17, 2006 BIRCH Release A1.98 o Bluejay has been upgraded to the version dated Jan. 27, 2006 o Artemis has been upgraded to v.8 o Taverna has been upgraded to v. 1.3.1. This version fixes problems which caused Taverna to crash with Java 1.5. o GDE has been upgraded to macGDE v. 2.1.5. In this version, the HELP button in each menu launches a standalone document viewer, rather than displaying the documentation in the menu itself. o The CopyOut and PasteIn commands for dGDE, GDE, mGDE and tGDE now use separate clipboard files. For example, the PastIn for tGDE will past in the most recent clipboard contents from tGDE, and PasteIn for dGDE will paste in the most recent clipboard contents from dGDE. o Leash has been upgraded to version 2.2. This version includes new command line parameters, -mpil and -mpif, which make it possible for Leash to take lists of data as input for SeqHound methods which only allow a single data item (eg. SHoundSequenceLength). Previously, leash had to be called for each item in the list. A number of dGDE method calls have been updated to take advantage of the increased efficiency of these parameters. o Added new features to BACHREST that gives the user more ways to narrow the list of enzymes and digests shown in the output. Searches can be limited to enzymes that generate 5' protruding, blunt or 3' protruding ends, or that have either symmetric or asymmetric recognition sequences. The parameters LEASTFRAGS and MOSTFRAGS also allow you to only print digests with at least LEASTFRAGS fragments, or at most MOSTFRAGS. It is also possible to keep the output file small by setting PRINTFRAGS. When the number of fragments in a digest exceeds PRINTFRAGS, MULTIDIGEST will only print the number of fragments, rather than printing all of the fragments themselves. Finally, BACHREST now prints the values of these parameters in the header lines of the output file. The maximum sequence size allowed by BACHREST has been increased to 20,000,000, allowing most bacterial genomes to be read. However, for very large sequences, BACHREST must be used at the command line. GDE will only read sequences that are 750K or smaller. To avoid conflict with the Solaris 10 digest command, DIGEST has been renamed as MULTIDIGEST. MULTIDIGEST has been updated to read the new BACHREST output file format. Also, see what else is new with BIRCH, from the presentation at the Plant and Animal Genome Conference XIV: http://home.cc.umanitoba.ca/%7Efrist/Seminars/pag14/pag14.html ======================================================== The latest release of BIRCH (A1.98) is available at the BIRCH Web site http://home.cc.umanitoba.ca/~psgendb under the link 'BIRCH Administrator's Guide'. BIRCH now available for Solaris/AMD64 Submitted by Brian Fristensky; posted on Tuesday, January 03, 2006 ======================================================== BIRCH Release A1.96 BIRCH now supports the Solaris/AMD64 platform. With the latest release, binaries for most BIRCH core programs are now available for Sun's Solaris/AMD64 machines. In mixed platform environments, BIRCH users can now run most BIRCH applications transparently with respect to whether they are logged into a Linux-Intel, Solaris-Sparc or Solaris-AMD64 host. ======================================================== The latest release of BIRCH (A1.96) is available at the BIRCH Web site http://home.cc.umanitoba.ca/~psgendb under the link 'BIRCH Administrator's Guide'. A1.96 Release Notes --------------------------- December 29, 2005 o To simplify the process of making BIRCH documentation Web-accessible, the birchconfig URL Builder has additional suggested choices for possible locations of the BIRCH web site and Home directories. o BIRCH now supports the solaris-amd64 platform. Some programs are not available for solaris-amd64, including mapmaker and primer3. o birchconfig.csh has been replaced by 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 Submit Archive Subscribe