09 May 17 GenBank 219.0 is now online.
02 May 17 BIRCH has been upgraded to Version 3.40.
20 Oct 15 Jalview has been upgraded to version 2.9.0b2.
06 Oct 15 GenBank 209.0 is now online.
22 July 15 BIRCH has been upgraded to Version 3.10.
4 May 15 BIRCH has been upgraded to Version 3.00.
06 Oct 14 The local FASTA-formatted copy of GenBank has been replaced with
the most recent BLAST-formatted copy, GenBank Release 203.0.
1 Sep 12 BIRCH has been upgraded to Development version September 1, 2012.
6 Aug 12 BIRCH has been upgraded to Development version August 6, 2012.
1 May 12 GenBank 189.0 is now online.
29 Apr 12 BIRCH has been upgraded to version 2.9.
1 Apr 12 BIRCH has been upgraded to the latest Development version,
dated March 29, 2012. This Development version
has been tested extensively. However, if you discover errors,
please send an email to firstname.lastname@example.org with a precise
description of the problem.
4 Oct 11 GenBank 185.0 is now online.
25 Sep 11 BIRCH has been upgraded to yesterday's Development version
Please report problems to email@example.com.
24 Sep 11 BIRCH will be temporarily unavailable due to an upgrade, Sunday Sep 25 from 9:00 - 12:00
13 Jul 11 GenBank 184.0 is now online.
25 Mar 11 GenBank 182.0 is now online.
3 Jan 11 GenBank 181.0 is now online.
16 Sep 10 GenBank 179.0 is now online.
19 Mar 10 GenBank 176.0 is now online.
11 Oct 08 GenBank 173.0 is now online.
15 Aug 09 GenBank 172.0 is now online.
7 Jun 08 GenBank 165.0 is now online.
6 Jun 08 Taverna has been upgraded to version 1.7.1.
1 Nov 07 GenBank 162.0 is now online.
8 May 07 GenBank 159.0 is now online.
2 May 07 Taverna has been upgraded to version 1.5.1.
24 Feb 07 GenBank 158.0 is now online.
15 Feb 07 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.
13 Feb 07 Bluejay has been upgraded to version 0.7.
30 Jan 07 The Phylip PARS program, for parsimony analysis of marker data
can now be run from mGDE.
2 Jan 07 GenBank 157 is now online.
30 Nov 06 GenBank 156 is now online.
8 Oct 06 GenBank 155 is now online.
22 Sep 06 Stem has been upgraded to 1.2.1. See
3 Sep 06 Bluejay has been upgraded to the version dated Aug. 25, 2006
11 Jul 06 The EMBOSS package has been upgraded to Version 3.0.0.
28 Jun 06 GenBank 154 is now online.
3 Jun 06 weighbor: Neighbor-Joining program which produces more reliable
trees than traditional NJ. Now available as an option in GDE.
21 May 06 GenBank 153 is now online.
11 May 06 o A number of Microarray programs have been installed, and
are available for testing. See:
Comments can be sent to firstname.lastname@example.org.
10 Apr 06 o The Help buttons in GDE menu items can now display documentation
files of any type, not just text.
o BACHREST can now narrow the search for restriction enzymes
to specific types of sites (eg. symmetric, blunt, 3' protruding
etc.) BACHREST can also read sequences up to 20 million nucleotides.
This feature is only available at the command line.
o The GDE 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
o The digest program, for calculating multienzyme restriction
digests, has been renamed 'multidigest'.
24 Feb 06 GenBank 152 is now online.
28 Jan 06 BIRCH has been updated to Version A1.97. With this version, GDE
has been broken up into four specialized interfaces:
gde - sequences
dgde - lists of identifiers (eg. Accession, GI, TaxID)
mgde - molecular markers
tgde - phylogenetic trees.
See GDE Overview
29 Nov 05 GenBank 150 is now online.
23 Aug 05 GenBank 149 is now online.
28 Jul 05 GenBank 148 is now online.
6 May 05 GDE has been updated to fix several bugs. Most importantly, GDE
no longer crashes when cutting blocks of a sequence alignment
spanning more than one window, or when attempting to cut when
sequence protections are on. Please report any problems with
GDE to email@example.com.
6 May 05 GenBank 147 is now online.
14 Feb 05 The BIRCH documentation is in the process of being re-organized.
See the new links for finding programs by category, programs
by package, and an alphabetical program index. At present some
programs are missing, but will be added to these pages over
the next few weeks.
27 Jan 05 PHYLIP has been upgraded to v3.63. This upgrade vastly expands
number of programs and features available for running PHYLIP
3 Jan 05 GenBank 145 is now online.
19 Nov 04 GenBank 144 is now online.
28 Aug 04 GenBank 143 is now online.
11 Aug 04 The BLAST programs are now available through the GDE interface.
This implementation runs searches remotely at NCBI, returning
the results to GDE.
13 Jul 04 The complete EMBOSS package is on the system as part of
the local implementation of the Canadian Bioinformaics
3 Jul 04 GenBank 142 is now online.
16 May 04 TCOFFEE, a sophisticated multiple alignment program, is now
available at the command line (t_coffee) or through GDE. See:
30 Apr 04 GenBank 141 is now online.
9 Mar 04 GenBank 140 is now online.
25 Jan 04 GenBank 139.0 is now online.
2 Nov 03 Entrez and Sequin have been upgraded to the latest versions.
Entrez - text search of NCBI databases
Sequin - annotate and submit new sequences to GenBank
26 Oct 03 GenBank 138.0 is now online.
27 Sep 03 GenBank 137.0 is now online.
24 Jun 03 GenBank 136.0 is now online.
19 Apr 03 GenBank 135.0 is now online.
11 Mar 03 Artemis is a DNA sequence viewer and annotation tool that allows
visualisation of features in a rich graphic display.
5 Mar 03 tacg3.6b has been installed. tacg searches for restriction
sites, as well as patterns such as transcription factor
binding sites. Results are displayed in tabular form,
on sequence, and on maps. tacg can be run from GDE.
3 Mar 03 The Staden Package has been updated to version 2002.0
17 Feb 03 GenBank 134.0 is now online.
8 Jan 03 GenBank 133.0 is now online.
6 Dec 02 If you have the generic workspace menu, and you would like to
switch to the BIRCH custom menu, type
'/home/psgendb/admin/menusetup'. Most BIRCH users already have
the BIRCH menu, which includes the "Molecular Biology" submenu.
17 Nov 02 GenBank 132.0 is now online. With this release, the GenBank
database has been relocated from /home/psgendb/GenBank to
a separate filesystem, /local/genbank. This change should
be completely transparent to BIRCH users.
13 Nov 02 GenBank will be unavailable beginning around 13:00 Saturday
to allow replacement of a defective disk.The database will
be re-downloaded, beginning around 18:00, and the full
database should be available by early Monday morning.
Sequences can be retrieved using entrez, and fasta searches
can be done at http://alpha10.bioch.virginia.edu/fasta/
11 Nov 02 GenBank 132.0 is now online. Due to a technical problem,
the file gbest166.seq, containing 71,542 ESTs (~ 0.5%
of ESTs) is missing. It will be restored as soon as possible.
9 Nov 02 The NCBI tools entrez, sequin and Cn3D have been upgraded.
Due to a problem with the OpenGL libraries, Cn3D is
not currently working.
5 Oct 02 Some BIRCH directories have been reorganized, which
should be entirely transparent. However, if any programs
stop working, send a message to firstname.lastname@example.org.
11 Sep 02 Entrez has been updated. This version correctly handles the new
GenBank LOCUS line format.
7 Sep 02 GenBank 131.0 is now online.
2 Jul 02 FASTA 3.4 has been installed. See $doc/fasta/readme.v34t0.
1 Jul 02 GenBank 130.0 is now online.
13 May 02 A graphic interface to splitdb has been added to the GDE File menu.
5 May 02 PIR 72.02 is now online.
29 Apr 02 GenBank 129.0 is now online.
23 Feb 02 GenBank 128.0 is now online.
29 Jan 02 A bug in FETCH caused PIR files to be written with the .gen file
extension, when sending each entry to separate files (-f). Files
are now correctly written with the .pir extension.
25 Jan 02 PIR 71.01 is now online.
2 Jan 02 GenBank 127.0 is now online. Beginning with this release, all
GenBank entries have a new LOCUS line format. So far all programs
tested work with the new format. Please report problems to
email@example.com. See $doc/GenBank/relnotes.txt
3 Sep 01 GenBank 125.0 is now online.
22 Jul 01 The FASTA programs have been updated to version 3.3t09.
1 Jul 01 GenBank 124.0 is now online.
25 Jun 01 A new version of readseq has been installed. Readseq is used
by GDE to translate sequences from one format to another,
so this could affect almost any program run by GDE.
Please report any problems with GDE to firstname.lastname@example.org.
2 Jun 01 GenBank 123.0 is now online.
15 Feb 2001 The BIRCH filesystem will be moved to allow for expansion.
On Sunday morining Feb. 18, BIRCH programs and files will
be unavailable. Users logging in during this time will also
not have the BIRCH workspace menu and customized command
16 Dec 2000 GenBank 120.0 is now online.
Aug 2000 ACEDB has been upgraded to version 4.71.
May 2, 2000 A bug which caused discrete data parsimony
programs (dollop, mix) to crash when using more
than 50 characters per sequence has been fixed. This
only affected programs run through GDE.
Mar. 12 2000 GenBank 116.0 is now online.
Nov. 14, 1999 GenBank 114.0 is now online. Note that sequences in the
RNA division have been incorporated into other divisions.
See BIRCH Website under 'Databases, GenBank'
Aug. 26, 1999 NEW COURSE: 39.709 Topics in Genetics - BIOINFORMATICS
Jan. 2000. See BIRCH Web site.
July 15, 1999 TraceView - ABI DNA chromatogram viewer
July 2, 1999 GenBank 112.0 is now online.
June 3, 1999 Sequin 2.9 has been installed.
May 9, 1999 GenBank Release 111.0 is now online. This release splits
up some divisions (plants, gss, htg, invertebrates ...)
into several files each. I have made some minor software
changes to accommodate the splits. However, if there are
errors during database searches, please report
them by email to 'email@example.com'. Give full details.
15 Apr 98 PIR Release 55 is now online.
6 Apr 98 GenBank Release 105 is now online.
18 Mar 98 The GDE menu for ALSCRIPT now allows you to print alignments
using custom colors for nucleotides or amino acids. Also,
dashes or blanks can be chosen as gap characters.
12 Mar 98 Sequin 2.45 has been installed.
25 Feb 98 Previously, GDE would strip leading gaps from the beginning
of an alignment before sending to CLUSTALX. This has been
24 Sep 97 fastDNAml has been modified such that when bootstrapping is
done, both a consensus treefile and a raw treefile, containing
all trees generated by each replicate, will be created.
24 Sep 97 SEQUIN 2.28 is now online.
15 Sep 97 In the next few weeks, I will change GDE to use CDE-specific
tools such as the dtpad text editor and the dtterm terminal
window. These will replace the corresponding OpenWindows
tools, textedit and shelltool. If you have not already
switched over to CDE, now is a good time to do so.
See 'Using CDE' at the BIRCH web site for more information.
19 Aug 97 SEQUIN Version 2.20 has been installed.
19 May 97 clustalx - X-windows interface to clustalw. Read news
on man.molbio, or see
16 May 97 Primer3 - PCR primer design program, now available as a
batch command and through GDE. Read news in man.molbio.
3 Apr 97 A bug preventing treetool from using fonts other than the
default font (Helvetica 12pt) has now been fixed.
13 Mar 97 GenBank 99.0 is now online. Two new divisions include:
HTG - High Throughput Genomic seq., GSS - Genome Survey Seq.
See $doc/GenBank/gbrel.txt for more info.
19 Jul 96 GenBank 95.0 is now online.
31 May 96 BIRCH WWW site: http://home.cc.umanitoba.ca/~psgendb
4 May 96 phylo_win, an X-windows-based program for constructing
phylogenies from aligned sequences, is now on line.
26 Apr 96 SEQUIN, a program for entering and submitting sequence
data to GenBank is now online. SEQUIN is only available
to X-windows users. To run type 'sequin'.
24 Apr 96 NCLEVER, a text-based interface to ENTREZ, is now online.
NCLEVER is run by typing 'nclever'. For documentation,
type 'man clever' or see $doc/clever/clever.doc.
20 Apr 96 ENTREZ, the NCBI database search program, is now online.
ENTREZ provides sophisticated search methods for finding
information in MEDLINE, GenBank, and various protein
databases. Just type 'entrez' to start. Entrez is only
available to X-windows users. See $doc/entrez/entrzdoc.txt.
27 Jan 96 FINDKEY has been fixed to work with recent changes in the
GenBank EST division. Queries to GenBank EST's should now
7 Jan 96 GenBank Release 92.0 is now online.
4 Jan 96 RESTDIST, a program for calculating genetic distances
using RFLP data, is now online. RESTDIST is part of
the PHYLIP package. See $doc/Phylip/restdist.tex.
7 Jun 95 REBASE version 506 is now online.
31 May 95 GenBank and PIR files have been fixed, and retrieval of
entries using FETCH has been re-enabled.
Report any problems with FETCH to firstname.lastname@example.org.
31 May 95 Due to an error in file conversion, the annotation for GenBank
and PIR files will be inaccessible until tomorrow.
Until GenBank and PIR annotation files are re-configured,
retrieval by FETCH will not be available. FASTA searches
can still be done.
30 May 95 Starting at 20:00 tonight, new versions of database programs
will be installed, and GenBank and PIR files will be converted
to accomodate them. Some database divisions will be unavailable
during the conversion.
16 Feb 95 GenBank Release 87.0 is now online.
4 Feb 95 PIR Release 43.0 is now online.
28 Dec 94 New versions of GETLOC, SPLITDB, and GETOB have been installed,
which could affect the functions of FINDKEY, FETCH and FEATURES.
Please report any problems with these programs to 'frist'.
18 Dec 94 GenBank Release 86.0 is now online.
8 Aug 94 fastDNAml, a fast version of the PHYLIP dnaml, is now online.
See documentation files in $doc/Phylip/fastDNAml. Also available
30 Jul 94 PIR Release 41.0 is now online.
12 Jul 94 GDE now has additional online documentation. See man.molbio
12 Jun 94 GenBank Release 83.0 is now online.
10 Apr 94 GenBank Release 82.0 is now online.
12 Mar 94 Two new pattern matching programs are available:
signal - scans Transcription Factor Database (Ghosh) with a
test sequence. see $doc/Signal_Scan for documentation.
gp - GeneParser. Searches for exons & introns in a DNA seq.
9 Mar 94 SEMINAR: THE GENETIC DATA ENVIRONMENT (AND OTHER HOOKS INTO
THE GLOBAL BIOMATRIX) Wed. Mar. 16, Armes 208, 3:45pm
Speaker: Dr. Brian Fristensky, Plant Science
19 Feb 94 GenBank Release 81.0 is now online.
8 Feb 94 Many of the XYLEM programs have been updated. Also, XYLEM menus
under GDE now allow for a more seamless flow of data between
tasks. See man.molbio.
8 Jan 94 The new FEATURES option -U automatically processes all entries,
eliminating the need for a namefile. see $doc/xylem/features.doc.
13 Dec 93 GenBank Release 80.0 is now online.
7 Dec 93 In GDE, ALIGN provides several output formats, including
the ability to read the alignment back into GDE.
29 Nov 93 NUMSEQ, BACHREST, P1HOM, P2HOM, D3HOM and D4HOM can now be
run from GDE.
15 Nov 93 PIR Release 38.0 is now online.
However, some index files were not available for downloading.
These will be obtained as soon as possible.
14 Oct 93 GenBank Release 79.0 is now online.
2 Oct 93 GDE2.2 has been installed. Revisions are documented in the
PostScript file $doc/GDE/GDE2.2_manual.ps.
12 Jul 93 GenBank Release 77.0 is now on line.
29 Jun 93 MASE appears to be working alright. Report any problems to
11 Jun 93 MASE temporarily out of service. See man.molbio.
15 May 93 Bachrest can now read REBASE. See $doc/fsap/rest.doc.
24 Mar 93 FETCH can now work with user-created database subsets.
23 Mar 93 PHYLIP Version 3.5 has been installed. See man.molbio,
20 Mar 93 PIR Release 35.0 is now online.
19 Mar 93 GenBank Release 75.0 is now online.
22 Feb 93 OSP - Oligonucleotide Selection Program now available for
both text-based terminals ('osp') and X-windows ('ospX').
30 Dec 92 A new version of readseq has been installed.
19 Dec 92 GenBank Release 74.0 is now online. See man.molbio for changes
in this release.
18 Dec 92 GenBank Release 74.0 will be downloaded tonight. Access to
GenBank may be delayed or blocked during this time. Things
should be back to normal Saturday morning.
17 Dec 92 Upcomming change in GenBank divisions: ORG (organelle) division
will be deleted, and a new division, EST (expressed sequence tag)
will be created with Release 74.0, to be installed this weekend.
10 Nov 92 NEW NEWSGROUP: man.molbio. Topics: 1) items of general interest
to molecular biologists in Manitoba 2) items relevant to BIRCH
To subscribe type 'g man.molbio' in rn. The introductory message
for this newsgroup is stored in $doc/man.molbio.tex.
29 Oct 92 PIR Release 34.0 is now online.
1 Oct 92 The BIRCH databases and software will be unavailable after 23:00
on Sat. Oct. 23 while files are transferred to a new server.
Service should be restored by Sun. morning.
19 Sep 92 GenBank Release 73.0 is now on line.
4 Sep 92 Version 3.0 of LiMB (Listing of Molecular Biology databases)
is now online.
4 Sep 92 Email retrieval of GenBank entries has shifted to the National
Center for Biotechnology Information (NCBI). Use
'email@example.com' instead of 'firstname.lastname@example.org'.
28 Jul 92 FEATURES can now be run entirely from the command line. See
23 Jul 92 CLUSTALV, a multiple sequence alignment program, is now
online. To run, 'clustalv'. See $doc/clustalv/clustalv.doc
for more information. Note: the 'HELP' option of clustalv
is not yet available.
18 Jul 92 PIR Release 33.0 is now online.
23 Jun 92 fasta version 1.6c2 is now installed.
20 Jun 92 GenBank Release 72.0 is now online.
19 Jun 92 The BIRCH USER'S GUIDE is now available in PostScript form in
the file $doc/BIRCH.ps. To print, type 'printdoc $doc/BIRCH.ps'.
16 May 92 FEATURES and GETOB now write a feature expression to a file
for each feature extracted. See $doc/xylem/features.doc and
16 May 92 PIR Release 32.0 is now online.
28 Apr 92 A problem was found in the new version of the FSAP programs
that perform filename expansion. The old version of the
programs has been restored, until the error can be fixed.
25 Apr 92 All FSAP programs (eg. NUMSEQ, D3HOM) can now perform filename
expansion. That is, filenames may include any construct, such as
environment variables, that can be interpreted by the shell.
Examples: $dat/fsap/test.seq, ~/seq/pMU1.dna, ../SYNBLKSP.gen.
For a list of FSAP programs, see $doc/fsap/FSAP.doc.
5 Apr 92 GenBank Release 71.0 is now online.
6 Mar 92 "Zen and the Art of the Internet: A Beginner's Guide to the
Internet" (~100 pages) can be printed on the PostScript printer.
Type 'printdoc $doc/network/zen-1.0.ps'.
3 Mar 92 GENEID Email server: Prediction of exons and gene structure.
3 Mar 92 REFORM has been modified for easier compatibility with MASE and
PIMA. See $doc/xylem/reform.doc.
1 Mar 92 New Programs: PIMA (Pattern-Induced Multi-sequence Alignment)
produces robust multiple alignments based on common motifs shared
among clusters of sequences. Alignment files are directly read-
able by MASE. Pattern files produced by PIMA can be used as
input for PLSEARCH (Pattern-library search) for similarity
comparisons far more sensitive that fasta.
See $doc/MBCRR/pima/ and $doc/MBCRR/plsearch/.
17 Feb 92 A new release of the BIRCH User's Guide is now available. Master
copies for Xeroxing can be borrowed from Dr. Brian Fristensky,
Agriculture W200A, 474-6085 or Dr. Klaus Wrogemann, Biochemistry,
HSC, 788-6701. The WordPerfect file can also be obtained by
anonymous FTP to ccu.umanitoba.ca in the pub/psgendb directory.
11 Feb 92 PIR Release 31.0 is now online.
10 Feb 92 Availability of the PIR database may be interrupted tonight
and tomorrow morning as updates are downloaded.
9 Feb 92 GenBank Release 70.0 is now online.
7 Feb 92 All BIRCH programs will be unavailable for a 3 hr. period on
Sat. 8, somewhere between 14:00 and 20:00 for an upgrade to a
larger filesystem. Following the upgrade, GenBank Release 70.0
will be downloaded and installed. While this should not interfere
with access to GenBank, there may be some delays in accessing
GenBank data Saturday night and Sunday. All other BIRCH resources
will be available after 20:00 Saturday.
6 Feb 92 REMINDER: Each user should have his/her own userid. If you are
using someone else's account, get your own. It's free!
See your departmental account administrator for more info.
3 Feb 92 AUTHORIN 1.2 is now available. To receive disks for copying,
send an email message to 'frist', indicating the media (3 1/2"
or 5 1/4" floppy) and your mailing address. AUTHORIN can also
by obtained by anonymous FTP to genbank.bio.net, in the
directories pub/dos/authorin or pub/mac/authorin. All sequences
submitted to GenBank or EMBL should be submitted using AUTHORIN.
30 Jan 92 findkey can now search user-generated database subsets.
16 Jan 92 fasta version 1.6b2 has been installed. This version fixes
several bugs, and adds some options to existing programs.
Documentation has been reorganized into an easier-to-read
format. Type 'printdoc $doc/fasta/fasta16.nroff' to print this
document, or 'less $doc/fasta/fasta16.doc' to browse through
it on the screen.
14 Dec 91 Because of recent changes in the way the PIR database
handles accession numbers, splitdb has been modified to
accept either the old or new formats. This should be trans-
parent to most users.
24 Nov 91 Previously, FINDKEY wrote files in the form 'name.ex1.ex2'
where ex1 and ex2 are file extensions. In some cases, .nam
files generated by FINDKEY were not properly handled by FEATURES.
FINDKEY now uses the form 'email@example.com'. See $doc/xylem/findkey.doc
17 Nov 91 A feature/bug of FETCH that retrieved all entries whose names inclu-
ded the names of entries requested has been fixed. FETCH will now
retrieve ONLY those entries specifically requested.
15 Nov 91 All Pascal programs should now run on all workstations.
14 Nov 91 Due to installation problems with Pascal libraries, most programs
in FSAP, XYLEM PHYLIP will only run on ccu. Exceptions are NUMSEQ,
FETCH, GETLOC and SPLITDB, which now run on all workstations.
Computer Services should fix this problem soon.
14 Nov 91 Seminar Announcement - BIRCH: A COMPUTING RESOURCE FOR MOLECULAR
BIOLOGY, Tue. Nov. 26, 3:30pm, Engineering 234B, Ft. Garry
Campus. Speaker: Dr. Brian Fristensky
12 Nov 91 PIR Release 30.0 is now installed.
11 Nov 91 readseq - This program, by Don Gilbert at Indiana Univ., can
read sequences in any of 13 different formats (eg. GenBank,
EMBL, GCG, Phylip) and write them in another format. Type
'readseq' and try it out.
8 Nov 91 The collection of molecular biology programs and databases will
henceforth be referred to as BIRCH (BIological Research Computer
Hierarchy). A comprehensive manual detailing the use of BIRCH is
now available. Contact Brian Fristensky x-6085 or frist.
30 Oct 91 All documentation files can now be printed using the command
'printdoc filename'. Printouts can be picked up at the output
window on the sixth floor of Engineering. Allow ~ 20min.