1. SPOREs Specialized Programs of Research Excellence Ryan Landy Qinyan Pan -SAIC 2003 NCICB Jamboree

2. Agenda Introduction to the SPOREs Protocol Submission Portal In-depth Look at the components of the system Future Development – common components SPOREsources Website Re-use of Dynamic and Static Content http://sporesprotocols.nci.nih.gov http://sporesources.nci.nih.gov

3. SPOREs Protocol Submission Portal http://sporesprotocols.nci.nih.gov

4. SPOREs Protocols Application ….a brief introduction

5. Protocol Submission Researchers can submit clinical trials protocols via the Protocol portal Researchers must specify the protocol title, organ site, protocol and grant number, status, CTA/IND #, and protocol endpoints http://sporesprotocols.nci.nih.gov

6. PI/Site Information Information on the protocol SPORE Directors, Primary Performance Site, Study PI’s, and participating sites should be included Users have the ability to add new Participating Sites and Study PI’s to the system

7. Trial Information Trial information including type of trial, phase, start/end dates, treatments, dosage, and regiment can be specified Protocol documents can be uploaded

8. Accruals Actual accrual statistics for each trial can be entered There are 6 races with the appropriate genders

9. Protocol Review All information can be reviewed prior to protocol submission Researchers can then elect to make changes or submit the trial

10. Protocol Search Researchers can search for clinical protocols by Title, Phase, Agent, and Organization Basic (above) and Advanced (below) searches are available

11. Search Results Admin Search Results page (shown above) allows for the enabling/disabling of trials Protocol search results include links to more detailed information

12. Trial Details Detailed Information about a Trial is displayed here The Protocol Document may also be downloaded if the submitter wished to make the document available

13. Documentation Use Cases Object Model Release Notes JavaDocs Will all be available on the WebDev Portal, to be released in the near future

14. SPOREs Protocol Submission Portal In-depth look at Application’s architecture

15. SPOREs Architecture Highlight Utilizes n-tier architecture design for reusability, portability and scalability Integrates with technologies developed at NCICB -- caBIO/ncicb, GEDP, caMDB, caIMAGES Extended caBIO components provides the transaction based data exchange

16. SPOREs Architecture

17. The Web Tier Design based on Model-View-Controller 2 (MVC2) pattern. The Controller delegates requests to an appropriate handler. Each handler acts as an adapter between the request and the Model. The Model represents, or encapsulates, an application's business logic or state. Control is usually then forwarded back through the Controller to the appropriate View.

18. caBIO /ncicb Tier NCICB open-source backbone infrastructure The caBIO /ncicb objects simulate the behavior of actual Clinical Protocol components such as clinical trials, agents, treatment schedules, end points, accruals, trial roles, etc. Provide object relational mapping that is optimized for the data warehouse queries Provides the bi-directional data exchange

19. The Persistence Tier Independent persistence of the domain objects. Allows the data layer to migrate as necessary to increase performance or access to new data stores without impacting the object layer. Includes RDBMS, flat files

20. SPOREs Object Model

21. SPOREs Future Development User friendly Admin Features providing Clinical Trial Protocol management tool SPOREs PIs/Sites management tool Linkage between protocols with EVS and other research information system Reusable components for security and logging

22. Security Components Develop security components to provide: Authentication Authorization/Access Control Confidentiality Integrity Auditing

23. Logging Components Plan to utilize an open source logging API to achieve: Thread safety. Efficiency and flexibility. Support for multiple logging levels. Configurable logging formats. Ability to enable/disable logging. Automatic log file rollover.

24. SPOREsources Website http://sporesources.nci.nih.gov

25. SPOREsources Website Pre-Clinical Models Microarray Clinical Trials Genomic Tools Resources Communication http://sporesources.nci.nih.gov Mixture of Static and Dynamic Content

26. Pre-Clinical Models SPOREs View of the Cancer Models Database http://sporesources.nci.nih.gov/animalmodels/index.jsp

27. Microarray Resources DC static content is displayed in the SPOREs Framework Using Zope DTML Methods to pull the data into the site Little duplication Content Sharing among Zope sites (first zope site to do this) re-use of static content

28. CMAP Clinical Trials 1.Search 2.List Results 3.View Details #1 #2 #3 Re-use of Dynamic Components

29. CMAP Clinical Trials Search for Protocols by Keyword in title, Phase, Agent, or Lead Organization (AND) List of results show basic details of the protocol (above) Details page has in-depth Information about the protocol (image below) See cmap.nci.nih.gov more information Re-use of Dynamic Components

30. Genomic Tools Resources linking To the CGAP website http://cgap.nci.nih.gov Genes, Chromosomes, Tissues, and Pathways

31. Resources caImage Search Submit http://cancerimages.nci.nih.gov/caIMAGE/index.jsp Mouse and human cancer histology image server.

32. Communication ListServ Collaboration Tool for Organ Site groups Email Based

33. Feedback Website Feedback Form Uses Python and a Zope Mail Host First NCICB Website to offer this

34. ReCap for SPOREs Protocol Portal: (re)Use of the NCICB/caBIO Clinical Trial Objects Extension of the GEDP API Development of Common Components (login and security) SPOREsources Website: Re-use of both Static and Dynamic NCICB Content Pulls resources from various NCICB Projects including: CMAP, CGAP, DC, MMHCC, Animal Models Extends Zope to allow content sharing among Zope sites Uses DTML methods to leverage CMAP features in a SPOREs Framework Great Example of inter-project communication and integration/code re-use

35. The End Ryan Landy Qinyan Pan -SAIC