The current release version of the Biology Workbench is 3.2. If you have used the Biology Workbench previously (before February 2000), you might know that the last version to see extensive use was 3.0, and you will be interested in the changes outlined here. If you are new to the Workbench, this page will not be very interesting to you, and you should proceed in good conscience. This is not a comprehensive list, but it does give most of the major changes.
3.0 sessions cannot be imported to 3.2. You need to contact the
to do this. If you have been automatically moved over from 3.0 at the old
Biology Workbench site, this conversion will have been done automatically
-- please check your account to see if the conversion was successful.
The SRS Database search has been replaced by Ndjinn
Multiple Database Search. Ndjinn is a text-based database engine,
and brief instructions on its use are provided on the setup page and in
the help file.
The MSASHADE alignment coloring program has been replaced by
BOXSHADE. BOXSHADE is a more complete implementation of the
Boxshade program, and many additional options are available in this module.
CLUSTAL_W, the module that drew rudimentary phylogenetic trees
from ClustalW generated tree files, has been replaced by many programs.
DRAWTREE draws unrooted phylogenetic trees from those ClustalW tree
files. DRAWGRAM draws "rooted" trees (the root is inferred) from
the ClustalW tree files. CLUSTALDIST draws ClustalW-generated
distance matrices, and CLUSTALTREE gives a text, "Clustal Format"
DNADIST and DNAPARS have been added for nucleic
alignments, to allow one to do the same analyses that PROTDIST
and PROTPARS do on protein alignments
MOTIFGREPDB and MOTIFGREP have been replaced by
PATTERNMATCH and PATTERNMATCHDB
The View tool now allows the user to view the sequences or
alignments in various formats. In addition, it allows the user to download
a sequence (or all the sequences) in the format being viewed (the icons on
the title bar are for downloading -- see the help file for View for
The Add tool now can handle multiple-sequence files in the
Protein and Nucleic modes, and has a few additional options, like
color-coding of non-standard amino acid or nucleic coes. Read the help file
on Add and Edit for more information on the changes in these
Sessions are now handled somewhat differently. There is no
longer a "Default Mode" in which the data gets lost after exiting the
browser. Instead, one is placed in a "Default Session" when they enter
the Biology Workbench. All data in the default session is saved, unless
the user specifically removes it. The user is allowed to rename the default
session, which then creates a new, empty default sessions, and the data
that was formerly in the default session will be a session with the new
name that was specified. The default session can also be copied, but the
users will probably find it easiest just to create a new session and work
Multiple database selection is now available within all the
BLAST tools, the FASTA and SSEARCH tools, and
PSIBLAST has been added in a limited fashion. The ability to use
user-defined postition-specific matrices is not yet available, but otherwise
this should be a fairly useful implementation of PSIBLAST.
Minor updates and interface improvements have been made in a large number