BWBminAdministrative Web Interface for

Paracel BioView WorkBench

Frances TongMarc Rieffel, PhD

Paracel

Southern California Bioinformatics Summer InstituteSummer 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– creating new database sets– adding new members to sets– removing members from sets– deleting entire sets

• General Configuration : – setting of general system parameters

Each requires command line interface and/or manual editing of specific files

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

Beginning of file…

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 => ‘-------’,};

• 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 fasta file as Paracel BLAST formatted databaseLoad fasta file as GeneMatcher formatted database

Load fasta file as GeneMatcher formatted query

Input New Database Information

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

AcknowledgementsParacel

Dr. Marc Rieffel

Dave Meyer

Peter Wilson

Jun Qian

Mike Curtin

SoCalBSIDr. Jamil Momand

Dr. Nancy Warter-Perez

Dr. Sandra Sharp

Dr. Wendie Johnston

Jackie Heras

Fellow Interns

National Science Foundation : National Institutes of Health