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Genome Workbench

Genome Workbench. Chuong Huynh NIH/NLM/NCBI New Delhi, India October 1, 2004 huynh@ncbi.nlm.nih.gov. Obtaining GenomeWorkbench. Not officially released to the public Probably end of October 2004??? Beta version snapshots: ftp://ftp.ncbi.nih.gov/toolbox/gbench/. NCBI Genome Workbench.

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Genome Workbench

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  1. Genome Workbench Chuong Huynh NIH/NLM/NCBI New Delhi, India October 1, 2004 huynh@ncbi.nlm.nih.gov

  2. Obtaining GenomeWorkbench • Not officially released to the public • Probably end of October 2004??? • Beta version snapshots: • ftp://ftp.ncbi.nih.gov/toolbox/gbench/

  3. NCBI Genome Workbench

  4. Genome Workbench: Goals • Provide an interactive, client-side GUI • Provide full suite of annotation tools • Sequin does a lot of this • older code • primarily a submission tool • Provide a platform for visualization and analysis • Provide a platform that offers easy extensibility

  5. Why Client-Side? • Clients are now pretty fast • you can actually BLAST genomes on the client-side! • Access to private data • “If you can’t bring the data to GenBank, bring GenBank to the data!” • Not just private data – extend to private data sources, data management • Ability to mix and match analytical methods

  6. Application Architecture • Core application • provides application services, data management, standard dialogs and components • Plug-ins • handle most of the requests • everything is a plug-in

  7. Plugin Manager

  8. Core Application: MVC • MVC = Model / View / Controller • 30+ year old paradigm for applications • separates responsibilities of the application into discrete components • Genome Workbench uses this extensively • Model = Data being viewed • View = Viewers on this data • Controller = Application, editing framework • under construction

  9. Extensibility: Plug-Ins • Framework provides standard interfaces for defining, manipulating plug-ins • Dynamically loaded at runtime; Only loaded when needed • Plug-ins live in shared libraries • can have more than one plug-in per library • Don’t need to rebuild the entire application to add new features • Three types: • Data sources, Viewers, Algorithms

  10. Extensibility: Scripting • Wrap C++ interfaces with a bit of glue to make them available to scripting languages • Goals are two-fold: • obtain command console for scripting language • write plug-ins entirely in a scripting language • Focus initially on PERL, Python; intend to add others • Python completed; PERL almost completed

  11. Client-Side Benefits • Data Caching • data in GenBank is updated, but updates for individual sequences are infrequent • Pattern of use is frequently optimal for caching • BLAST request caching • BLAST requests valid for 24 hours • IDs unique, can be cached on the client-side • Directory Indexing • can index directories of files • can search by content, molecule type, IDs, etc.

  12. Some Functionality NOT Enabled • Only blastn works over the network • Choose From Other Documents Does not work in 20040712 build • Access to NCBI network through a proxy

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