1. NCBI Genome Workbench Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 15, 2004 huynh@ncbi.nlm.nih.gov Slides from Michael Dicuccio’s Genome Workbench June 21, 2004 talk

2. NCBI Obtaining GenomeWorkbench Not officially released to the public Beta version snapshots: ftp://ftp.ncbi.nih.gov/toolbox/gbench/

3. NCBI NCBI Genome Workbench

4. NCBI 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. NCBI 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. NCBI 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. NCBI Plugin Manager

8. NCBI 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. NCBI 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. NCBI 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 Not yet completed

11. NCBI 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. NCBI Some Functionality NOT Enabled Only blastn works over the network Choose From Other Documents Does not work in 20040712 build

13. NCBI Demo Main Application Window –List of loaded records Graphical Sequence Viewer –Navigation, GUI controls –Displayed features / annotations –Basic searching –Configuration properties Basic Sequence Analysis –Compositional Questions GC Content CpG Islands Protein, nucleotide molecular properties –Searching Pattern search Named sets of patterns (Kozak Scan) Restriction Sites ProSITE Open Reading Frames Simple Repeats

14. NCBI Demo Text Sequence Viewers –GenBank flat-file –FastA, ASN.1 –Feature Tables Advanced Sequence Analysis –Gene Prediction GNOMON – HMM-based gene predictor –Protein characterization Conserved domains Active regions –Coiled coils –Antigenic Sites Side-by-Side Data –Ensembl models –Tab-delimited data Alignments –Local BLAST –Network BLAST –Global (Needleman-Wunsch) alignment –Splign Miscellaneous Visualization Topics

15. NCBI Future Work Scripting –should be first option for extension Workspace Integration –only one top-level window –provide better integration of views, tools –provide better data organization Full editing features