spores specialized programs of research excellence ryan landy qinyan pan -saic 2003 ncicb jamboree

SPOREsSpecialized Programs of Research Excellence

Ryan Landy

Qinyan Pan

-SAIC

2003 NCICB Jamboree

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

SPOREs Protocol Submission Portal

http://sporesprotocols.nci.nih.gov

SPOREs Protocols Application

….a brief introduction

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

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

Trial Information

• Trial information including type of trial, phase, start/end dates, treatments, dosage, and regiment can be specified

• Protocol documents can be uploaded

Accruals

• Actual accrual statistics for each trial can be entered

• There are 6 races with the appropriate genders

Protocol Review

• All information can be reviewed prior to protocol submission

• Researchers can then elect to make changes or submit the trial

Protocol Search

• Researchers can search for clinical protocols by Title, Phase, Agent, and Organization

• Basic (above) and Advanced (below) searches are available

Search Results

• Admin Search Results page (shown above) allows for the enabling/disabling of trials

• Protocol search results include links to more detailed information

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

Documentation

• Use Cases

• Object Model

• Release Notes

• JavaDocs

• Will all be available on the WebDev Portal, to be released in the near future

SPOREs Protocol Submission Portal

In-depth look at

Application’s architecture

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

SPOREs Architecture

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.

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

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

SPOREs Object Model

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

Security Components

Develop security components to provide:• Authentication• Authorization/Access Control• Confidentiality• Integrity• Auditing

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.

SPOREsourcesWebsite

http://sporesources.nci.nih.gov

SPOREsources Website

•Pre-Clinical Models

•Microarray

•Clinical Trials

•Genomic Tools

•Resources

•Communication

http://sporesources.nci.nih.gov

Mixture of Static and Dynamic Content

Pre-Clinical Models

• SPOREs View of the Cancer Models Database

http://sporesources.nci.nih.gov/animalmodels/index.jsp

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

CMAP Clinical Trials

1. Search2. List Results3. View Details

#1

#2#3

Re-use of Dynamic Components

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

Genomic Tools

• Resources linkingTo the CGAP website

• http://cgap.nci.nih.gov

•Genes, Chromosomes,Tissues, and Pathways

Resources

• caImage

• Search

• Submit

• http://cancerimages.nci.nih.gov/caIMAGE/index.jsp

• Mouse and human cancer histology image server.

Communication

• ListServ

• CollaborationTool for OrganSite groups

• Email Based

Feedback

• Website Feedback Form

• Uses Python and a Zope Mail Host

• First NCICB Website to offer this

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

The End

Ryan Landy

Qinyan Pan

-SAIC