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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