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BWBmin Administrative Web Interface for Paracel BioView WorkBench

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

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BWBmin Administrative Web Interface for Paracel BioView WorkBench

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  1. BWBminAdministrative Web Interface forParacel 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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 ! …

  7. 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… ~ open and edit database configuration file for BioView Workbench

  8. 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

  9. 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

  10. General Configuration

  11. Database Management

  12. Load fasta file as Paracel BLAST formatted database Input New Database Information Load fasta file as GeneMatcher formatted database Load fasta file as GeneMatcher formatted query Loading Databases

  13. Modifying Databases

  14. Selectively remove databases Deleting Databases

  15. Loading Existing Databases onto BWB

  16. Creating Database Sets

  17. Removing Members from Database Sets

  18. Future Work • Construction of similar pages for managing: • Paracel Filtering Package • Preloaded queries • Score matrices • Building of release for clients

  19. Acknowledgements National Science Foundation : National Institutes of Health

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