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BWBmin
Administrative Web Interface for
Paracel BioView WorkBench
Frances Tong
Marc Rieffel, PhD
Paracel
Southern California Bioinformatics Summer Institute
Summer 2004
Funded by the National Science Foundation and the National Institutes of Health
Overview
• Paracel products
– Paracel BLAST
• Software for BLAST searching
– GeneMatcher
• Supercomputer for genetic algorithms (Smith-Waterman, etc)
– BioView Workbench
• Graphical interface for user to run Paracel BLAST and
algorithms on GeneMatcher.
• Goal : Develop a user-friendly web interface for
administration of BioView Workbench
BioView Workbench : Graphical User Interface
for Paracel BLAST and GeneMatcher Searches
• Search submission interface which lets you access Paracel
algorithms without entering the command-line environment
Administrative Tasks for
BioView Workbench
• Database management :
– loading new databases
– modifying existing databases
– deleting existing databases
Each requires
command
line interface
– creating new
database sets
– manual
adding new editing
members to
and/or
ofsets
specific files
– removing members from sets
– deleting entire sets
• General Configuration :
– setting of general system parameters
BWBmin : User-friendly alternative
• Web interface for admin tasks
• Highly awaited by biologists
• Built from scratch in 9 weeks
as a Webmin module
• Currently consists of 7 CGI
scripts written in Perl, HTML
and Javascript, a Perl module
and other setup files
Before BWBmin…
• command line usage
• Ex: loading a new database (UCSC Human Chromosome 11)
into Paracel BLAST and GeneMatcher
• adding to Paracel BLAST
• adding to GeneMatcher
• still not done yet ! …
~ open and edit database configuration
file for BioView Workbench
Go to the end of the file and
type in database information
according to the format:
Hash table :
‘Key’ => {
name => ‘-------’,
type => ‘----’,
seqcount => ‘----’,
date => ‘-----’,
btk => ‘--------’,
btkoracle => ‘-------’,
pb => ‘-------’,
};
Beginning of file…
• a web-based interface for system
administration for Unix developed by
Jamie Cameron
• anyone can develop and distribute their
own Webmin modules for any purpose
• open source at
http://webmin.com/download.html
Advantages of BWBmin
• Automates and makes admin tasks
for Paracel BLAST and GeneMatcher
more user friendly and faster
– Elimination of multiple steps
– No dealing with the syntax errors
that may result with the command
line interface and manual editing of
configuration files
General Configuration
Database Management
Loading Databases
Load
Input
New
Database
Information
Loadfasta
fastafile
fileas
asParacel
GeneMatcher
BLAST
formatted
database
formatted
database
Load fasta file as GeneMatcher
formatted query
Modifying Databases
Deleting Databases
Selectively remove databases
Loading Existing Databases onto BWB
Creating Database Sets
Removing Members from Database Sets
Future Work
• Construction of similar pages for
managing:
– Paracel Filtering Package
– Preloaded queries
– Score matrices
• Building of release for clients
Acknowledgements
Paracel
Dr. Marc Rieffel
Dave Meyer
Peter Wilson
Jun Qian
Mike Curtin
SoCalBSI
Dr. Jamil Momand
Dr. Nancy Warter-Perez
Dr. Sandra Sharp
Dr. Wendie Johnston
Jackie Heras
Fellow Interns
National Science Foundation : National Institutes of Health