SPOREs Specialized Programs of Research Excellence Ryan Landy Qinyan Pan -SAIC 2003 NCICB Jamboree.
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Transcript of SPOREs Specialized Programs of Research Excellence Ryan Landy Qinyan Pan -SAIC 2003 NCICB Jamboree.
![Page 1: SPOREs Specialized Programs of Research Excellence Ryan Landy Qinyan Pan -SAIC 2003 NCICB Jamboree.](https://reader033.fdocuments.us/reader033/viewer/2022051401/56649f3e5503460f94c5ed15/html5/thumbnails/1.jpg)
SPOREsSpecialized Programs of Research Excellence
Ryan Landy
Qinyan Pan
-SAIC
2003 NCICB Jamboree
![Page 2: SPOREs Specialized Programs of Research Excellence Ryan Landy Qinyan Pan -SAIC 2003 NCICB Jamboree.](https://reader033.fdocuments.us/reader033/viewer/2022051401/56649f3e5503460f94c5ed15/html5/thumbnails/2.jpg)
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.govhttp://sporesources.nci.nih.gov
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SPOREs Protocol Submission Portal
http://sporesprotocols.nci.nih.gov
![Page 4: SPOREs Specialized Programs of Research Excellence Ryan Landy Qinyan Pan -SAIC 2003 NCICB Jamboree.](https://reader033.fdocuments.us/reader033/viewer/2022051401/56649f3e5503460f94c5ed15/html5/thumbnails/4.jpg)
SPOREs Protocols Application
….a brief introduction
![Page 5: SPOREs Specialized Programs of Research Excellence Ryan Landy Qinyan Pan -SAIC 2003 NCICB Jamboree.](https://reader033.fdocuments.us/reader033/viewer/2022051401/56649f3e5503460f94c5ed15/html5/thumbnails/5.jpg)
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
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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
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Trial Information
• Trial information including type of trial, phase, start/end dates, treatments, dosage, and regiment can be specified
• Protocol documents can be uploaded
![Page 8: SPOREs Specialized Programs of Research Excellence Ryan Landy Qinyan Pan -SAIC 2003 NCICB Jamboree.](https://reader033.fdocuments.us/reader033/viewer/2022051401/56649f3e5503460f94c5ed15/html5/thumbnails/8.jpg)
Accruals
• Actual accrual statistics for each trial can be entered
• There are 6 races with the appropriate genders
![Page 9: SPOREs Specialized Programs of Research Excellence Ryan Landy Qinyan Pan -SAIC 2003 NCICB Jamboree.](https://reader033.fdocuments.us/reader033/viewer/2022051401/56649f3e5503460f94c5ed15/html5/thumbnails/9.jpg)
Protocol Review
• All information can be reviewed prior to protocol submission
• Researchers can then elect to make changes or submit the trial
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Protocol Search
• Researchers can search for clinical protocols by Title, Phase, Agent, and Organization
• Basic (above) and Advanced (below) searches are available
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Search Results
• Admin Search Results page (shown above) allows for the enabling/disabling of trials
• Protocol search results include links to more detailed information
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Trial Details
• Detailed Information about a Trial is displayed here
• The Protocol Documentmay also be downloaded if the submitter wished to make the document available
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Documentation
• Use Cases
• Object Model
• Release Notes
• JavaDocs
• Will all be available on the WebDev Portal, to be released in the near future
![Page 14: SPOREs Specialized Programs of Research Excellence Ryan Landy Qinyan Pan -SAIC 2003 NCICB Jamboree.](https://reader033.fdocuments.us/reader033/viewer/2022051401/56649f3e5503460f94c5ed15/html5/thumbnails/14.jpg)
SPOREs Protocol Submission Portal
In-depth look at
Application’s architecture
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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
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SPOREs Architecture
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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.
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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
![Page 19: SPOREs Specialized Programs of Research Excellence Ryan Landy Qinyan Pan -SAIC 2003 NCICB Jamboree.](https://reader033.fdocuments.us/reader033/viewer/2022051401/56649f3e5503460f94c5ed15/html5/thumbnails/19.jpg)
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
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SPOREs Object Model
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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
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Security Components
Develop security components to provide:• Authentication• Authorization/Access Control• Confidentiality• Integrity• Auditing
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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.
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SPOREsourcesWebsite
http://sporesources.nci.nih.gov
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SPOREsources Website
•Pre-Clinical Models
•Microarray
•Clinical Trials
•Genomic Tools
•Resources
•Communication
http://sporesources.nci.nih.gov
Mixture of Static and Dynamic Content
![Page 26: SPOREs Specialized Programs of Research Excellence Ryan Landy Qinyan Pan -SAIC 2003 NCICB Jamboree.](https://reader033.fdocuments.us/reader033/viewer/2022051401/56649f3e5503460f94c5ed15/html5/thumbnails/26.jpg)
Pre-Clinical Models
• SPOREs View of the Cancer Models Database
http://sporesources.nci.nih.gov/animalmodels/index.jsp
![Page 27: SPOREs Specialized Programs of Research Excellence Ryan Landy Qinyan Pan -SAIC 2003 NCICB Jamboree.](https://reader033.fdocuments.us/reader033/viewer/2022051401/56649f3e5503460f94c5ed15/html5/thumbnails/27.jpg)
Microarray Resources
• DC static content is displayed in the SPOREs Framework • Using Zope DTMLMethods 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
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CMAP Clinical Trials
1. Search2. List Results3. View Details
#1
#2#3
Re-use of Dynamic Components
![Page 29: SPOREs Specialized Programs of Research Excellence Ryan Landy Qinyan Pan -SAIC 2003 NCICB Jamboree.](https://reader033.fdocuments.us/reader033/viewer/2022051401/56649f3e5503460f94c5ed15/html5/thumbnails/29.jpg)
CMAP Clinical Trials
• Search for Protocols by Keyword in title, Phase, Agent, or LeadOrganization (AND) • List of results show basicdetails of the protocol (above)
• Details page has in-depthInformation about the protocol(image below) • See cmap.nci.nih.govmore information
Re-use of Dynamic Components
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Genomic Tools
• Resources linkingTo the CGAP website
• http://cgap.nci.nih.gov
•Genes, Chromosomes,Tissues, and Pathways
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Resources
• caImage
• Search
• Submit
• http://cancerimages.nci.nih.gov/caIMAGE/index.jsp
• Mouse and human cancer histology image server.
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Communication
• ListServ
• CollaborationTool for OrganSite groups
• Email Based
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Feedback
• Website Feedback Form
• Uses Python and a Zope Mail Host
• First NCICB Website to offer this
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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
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The End
Ryan Landy
Qinyan Pan
-SAIC