Databases and Systems

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In order to make wrapper development easier and standardize tool integration into
the Workbench, several files containing subroutines are included in the Workbench
tree. These files are generally “required” by all Perl wrappers, but the subroutines
may be extracted and revised to suit individual needs. While we recommend using
the standard subroutines wherever possible, we cannot fully predict the needs of users
for other non-standard tool specific routines. This concept is being refined for future
releases of the Workbench.
The central file for tool integration is the “html.pl” file, which contains the
necessary subroutines for communication with BW.cgi (the Workbench core CGI
program) and for passing configuration information to the wrapper scripts. This file
should be included at the beginning of all scripts using the “require” directive in Perl.
Tools wrappers may, however, require only a subset of the subroutines in the html.pl
file.
Sessions
Each time a user accesses the Workbench, a previous analysis session can be
resumed or a new one initiated. The role of the sessions is to maintain the state and
sequence of operations performed on the Workbench during an interactive session.
Sessions can be useful for both recalling previously performed operations as well as
for comparison with newer analyses. Essentially, sessions provide the history of the
Workbench use and can be updated, erased or permanently stored.
Databases
Almost all of the relevant biological sequence, structure and literature databases are
accessible from the Biology Workbench. The databases are federated by
identification of common objects and indexing each database based on these objects.
We use the SRS schema (Etzold and Argos, 1993) to store and access the databases
allowing them to be queried for multiple objects as well as combinations of objects
using Boolean operators on the query construction page. The Workbench also
permits nested Boolean queries.
To aid the integration of SRS indexed databases, the file “db_config.pl”
containing routines for parsing database directories and identifying available
databases is provided. These routines also extract important information on specific
databases to allow sequence information to be properly imported to the Workbench.
A database mirroring program has also been developed for the Biology
Workbench, which fetches databases as they are updated in their primary
repositories. The indexing and creation of Blastable sequence database files is done
locally each time new databases are retrieved. A complete list of all databases
available on the Workbench is presented in Appendix A.
Analysis Modules