2. Creating Smart Clients with the Collaboration Notebook Greg Quinn Principal Investigator Desktop and Mobile Data Management San Diego Supercomputer Center Greg Quinn Principal Investigator Desktop and Mobile Data Management San Diego Supercomputer Center

3. Data overload The Collaboration Notebook: a data management solution Smart client development framework Future work Data overload The Collaboration Notebook: a data management solution Smart client development framework Future work Topics

4. Science research: it’s about the DATA! Locally generated, e.g. observations of a researcher at the lab bench Theoretical data Archived local data, collected from many researchers Data in legacy databases Data from collaborators, both near and far Data from Internet sources such as NCBI (NIH) Locally generated, e.g. observations of a researcher at the lab bench Theoretical data Archived local data, collected from many researchers Data in legacy databases Data from collaborators, both near and far Data from Internet sources such as NCBI (NIH)

5. The Encyclopedia of Life Project More than 800 genomes that have been completely or partially sequenced For each publicly available protein sequence derived from genomic data, EOL attempts to locate structural domains and correlate this data with other publicly available sequence annotation A large amount of information for end-users to collate Data management app More than 800 genomes that have been completely or partially sequenced For each publicly available protein sequence derived from genomic data, EOL attempts to locate structural domains and correlate this data with other publicly available sequence annotation A large amount of information for end-users to collate Data management app

6. Many Excellent Online Data Sites

7. NCBI BLAST (~2 million sequences) updated nightly XML Protein NR BLAST

8. DATA OVERLOAD! Legacy and archived data Online data sources Collaborative research Research notes and observations

9. No meaningful way to store data No simple way to re-purpose online data No mechanism to share data Difficult to keep track of data acquired during an online session Resource-intensive searches frequently repeated When data is retrieved, it can be difficult to manipulate and/or search No simple way to annotate downloaded data DATA OVERLOAD!

10. The Collaboration Notebook A desktop application to better enable the scientific researcher and knowledge worker utilize network information resources and manage data Leverages features of Windows and the.Net development Powerful local db with search functionality “Knowledge” of data types through the use of Ontologies Ability to annotate stored data Peer-to-peer querying of stored data and annotations Data export capability to popular formats Unattended/automatic data updates via web services & HTTP User notification of new data Plugin API for data visualization components – c/w basic data viewers for popular Bio-data types, e.g. text, DNA seqs, etc. Smart client framework for SOAP-based web services Point-and-click interface to support Tablet PC’s and ink data types Leverages features of Windows and the.Net development Powerful local db with search functionality “Knowledge” of data types through the use of Ontologies Ability to annotate stored data Peer-to-peer querying of stored data and annotations Data export capability to popular formats Unattended/automatic data updates via web services & HTTP User notification of new data Plugin API for data visualization components – c/w basic data viewers for popular Bio-data types, e.g. text, DNA seqs, etc. Smart client framework for SOAP-based web services Point-and-click interface to support Tablet PC’s and ink data types

11. Local datastore personal database Data presentation and Smart client for network data services Data Sources XML doc

12. Report and paper preparation Group collaborationResearch data access, input & annotation P2P SOAP Services Web Interfaces Other Data Sources The Connected Research Environment

13. Data browser N-App availability P2P Collaboration group Fast search options Smart Client display area WinformsAvalon Embedded apps GUI Design schematic

14. Networked Data services N-App Collection PDB EOL NCBI Work bench … Collaboration Notebook N-Apps N-AppServer

15. Smart Client..? Local resources Connected Offline capable Intelligent deployment and update Local resources Connected Offline capable Intelligent deployment and update

16. SOAP services WebPages DB’s Data services Data service wrappers Local DB Collaboration subsystem Service wrapper manager Service wrapper LocalInstrumentation N-App Interface class Smart Client data Data changed event Available Services Run request Reference Indigo Collaboration Notebook

17. Stages in Smart Client Dev Write your application with Windows forms or Avalon (control library project) Reference Notebook interface class and Notebook data objects class to gain access to Notebook services (e.g. data access, persistence and retrieval) Write a wrapper for the online service (if not using a pre-existing one) Write a data translator to convert incoming data into internal canonical format Write your application with Windows forms or Avalon (control library project) Reference Notebook interface class and Notebook data objects class to gain access to Notebook services (e.g. data access, persistence and retrieval) Write a wrapper for the online service (if not using a pre-existing one) Write a data translator to convert incoming data into internal canonical format

18. Debugging Smart Clients Data Service Service wrapper Test Harness

19. Embedding a Pre-existing Application Create a new Class Library project in Visual Studio Add reference to executable Use Visual Studio object browser to determine available methods Add references to Notebook interface class and Notebook data objects class Create a new Class Library project in Visual Studio Add reference to executable Use Visual Studio object browser to determine available methods Add references to Notebook interface class and Notebook data objects class

20. Wrapper communicates with Embedded app Wrapper Data Service Service wrapper Lat/Long data WorldWind://lat=x&long=y System Clipboard Worldwind.menuItemEditPaste.PerformClick() N-App Notebook

21. Example N-Apps BLAST interface Winforms BioConductor Interface Avalon (XAML) World Wind Embedded BLAST interface Winforms BioConductor Interface Avalon (XAML) World Wind Embedded

22. BLAST interface BLAST – Basic Local Alignment Search Tool Several BLAST SOAP services available: NCBI PDB EBI DDBJ Unified interface to these services BLAST – Basic Local Alignment Search Tool Several BLAST SOAP services available: NCBI PDB EBI DDBJ Unified interface to these services

23. BLAST Interface Smart Client

24. Developed by Dr. Robert Byrnes Statistical analysis of microarray data can be used to determine up- and down-regulation of genes, expression signatures, etc. The Bioconductor package is a widely used set of biostats routines that can be used to analyze microarray data Written in “R” language Current GUI’s to use Bioconductor are relatively crude Microarray Data Analysis

25. XAML-based Applications <FlowPanelxmlns="http://schemas.microsoft.com/2003/xaml"> Hello World Hello World Click me! Click me! </FlowPanel> XAML public partial class MyPanel { public string Hello() public string Hello() { return "Hello!"; return "Hello!"; } } C# +

26. Bioconductor packages R Interpreter SQL SERVER XML Metadata Notebook App Avalon Control Microarray App Developed by Dr. Robert Byrnes Microarray Data Analysis

27. Developed by Dr. Robert Byrnes Microarray Data Analysis

28. .Net-based app’s can be embedded with no modification required Need to creatively use existing methods within the application for data analysis, persistence and retrieval Embedded Applications

30. Smart Clients Under Development Protein Data Bank (PDB) Next Generation Biology WorkBench National Ecological Observatory Network (NEON) Homeland Security projects Protein Data Bank (PDB) Next Generation Biology WorkBench National Ecological Observatory Network (NEON) Homeland Security projects

31. 2004 2005 2006 FIELD TRIALS & TESTING UCSD RESEARCH LABS SOCIAL MONITORING INTERNAL BETA TESTING BUG TRACKING PUBLIC N-APP DEV MICROARRAY DATA ANALYSIS APP GEOSCIENCES-BASED APP OTHERS… CHARTER N-APPS CORE APP DEV CORE FEATURES DATA PLUGIN API SERVICE PLUGIN API XAML DEV FRAMEWORK SQL SERVER FIXED INTERNAL DATA MAPPING ADVANCED FEATURES P2P COMMUNICATIONS INTEGRATION OF DATA MAPPING SOLUTION NOTEBOOK RUNTIME SERVICE BACKGROUND DATA UPDATES INTEGRATION INTO “LONGHORN” PLATFORM DATA MAPPING & DISTRIBUTED QUERY ONTOLOGY-BASE DATA MAPPING DISTRIBUTED QUERY OPTIMIZATION CROSS-DOMAIN QUERY ADVANCED QUERY PROCESSING LAB

32. Hands-on One Day Workshop: Date: October 2005 Location: San Diego Supercomputer Center Further info: notebook@sdsc.edu Date: October 2005 Location: San Diego Supercomputer Center Further info: notebook@sdsc.edu Creating applications with the Collaboration Notebook

33. Acknowledgements Blair Jennings (lead) Robert Byrnes Martin Dubcovsky Kevin Fowler Blair Jennings (lead) Robert Byrnes Martin Dubcovsky Kevin Fowler Programmers

34. Acknowledgements Dan Fay & Microsoft Research Mark Miller, SDSC The SDSC Synthesis Center Dan Fay & Microsoft Research Mark Miller, SDSC The SDSC Synthesis Center Project Support

35. Questions? Greg Quinn quinn@sdsc.edu http://www.notebookproject.org

36. © 2005 Microsoft Corporation. All rights reserved. This presentation is for informational purposes only. Microsoft makes no warranties, express or implied, in this summary.