caTissue Suite 2.0 Scope Detail

TBPT Workspace call

May 23, 2011

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Agenda

• Introduction

• Review of detail of caTissue scope

• Opportunities for involvement

• caTissue Suite code jamboree

• Questions and Answers

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2.1.1 Fix critical defects based on caTissue user community feedback (End user)

• In Scope

• Improve Bulk Operations

• Bulk Operations for Dynamic Extensions

• Minimal UI enhancements to order functionality

• Out of Scope

• Single page user interface for specimen entry

• User Role based Dashboards

• Specimen collection reminder service

• Enhancement to ‘Google like’ search

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2.1.1 Fix critical defects based on caTissue user community feedback (Technical)

• In scope

• DE modification/add without JBoss restart

• Improved Build Process with

• Build moved to NCI’s Build and Deployment Architecture (BDA)

• Dynamic Extension administration issues

• CAS related deployment issues

• Tech stack upgrade

• Jboss 5.1.x, JDK 1.6

• FireFox 4, IE 8 and 9

• Oracle 11g, MySQL 5

• caGrid 1.4, caCORE /CSM 4.2

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2.1.1 Fix critical defects based on caTissue user community feedback (Technical)

• In scope

• Enhance code architecture

• Enable local code additions (At Sites and Via Support Service Providers)

• Dependent on input from Code Jamboree (June 20/27)

• Auto generation of Java classes based on caTissue UML model

• Out of scope

• caGrid transfer support for large volume data

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2.1.2 Provide Additional Grid Service Types

• In Scope• Aggregate queries (count)

• Multiple queries on associations

• Returning data from more than one object

• Hierarchical queries of known depth

• Patient Age at collection

• Out of Scope• Other important time difference variables e.g. freeze time, ischemia time

• Hierarchical queries of arbitrary depth

• Temporal queries – e.g., queries of patient date – may require working with grid

team

• “group by” queries – limited by grid functionality

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Examples of query types

• Aggregate queries (count)• e.g. No of participants registered to a collection protocol

• Multiple queries on associations• e.g. Find specimens that were fixed in formalin 30 minutes or

less and were embedded in low melting point paraffin

• Hierarchical queries of known depth• e.g. Find all RNA extracts derived from specimens where the

tissue fixative was not formalin

• Patient age at collection• e.g. Find all specimens collected from participants older than

70

• 2.1.3 Biospecimen Identifier

• In Scope

• Develop specs for Global Specimen Identifier

• Develop Global Specimen Identifier Service

• Host the Service at NCI

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2.1.4 Integrate caTissue with Assay Systems including caArray

• In Scope

• Develop MAGE-TAB Export functionality in caTissue to caArray

• Use of Global Specimen Identifier in MAGE-TAB export

• Availability of MAGE-TAB content via API and Grid services

• Ability to place orders by API & Grid Services

• Out of Scope

• MAGE-TAB Format will not be available as a service, but content

available as above.

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2.1.5 Export specimen data into MAGE-TAB format

• In Scope

• Export data into MAGE-TAB format to caArray and other MAGE-

compatible systems

• Out of Scope

• Direct developer testing with other systems than caArray

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2.1.6.1 Provide an order submission service

• In Scope

• Make sure that every capacity in UI is available through the API and

grid service

• Create order

• Check order status

• Approve/reject order

• Out of Scope

• Order workflow support

• Ability to place orders based on specimen requirements defined in

distribution protocols

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2.1.7 Integrate caTissue with NES

• In Scope

• CTRP Integration, use NCI Enterprise Services (NES) as the source

of record for key objects such as Protocol, Person, and Organization

• Explore and possibly use NES organizational structure for caTissue

• Replace cancer group, department

• Out of Scope

• None

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2.1.7.1 Implement Specimen Management Services

• In Scope

• Extend caTissue client API to writable caGrid API

• Provide caTissue Domain Object Model as writeable API and grid

service

• Out of Scope• Exposure of metamodel level services

• e.g. creation of dynamic extensions via API & caGrid services

• This functionality is provided via XMI export & import

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2.1.8 Enhance grid enablement of Dynamic Extensions

• In Scope

• Streamline Dynamic Extensions data availability through the grid

• Import and Export of Dynamic Extensions

• Add auditing capabilities for add, edit and query of Dynamic

Extension data via all UI, API and caGrid interfaces e.g. PHI

• Ability to deploy dynamic extensions on the grid and API without

restarting JBoss server

• Out of Scope

• Creation of dynamic extensions via API and caGrid services

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2.1.9.1 Person and study registration integration with CTMS applications

• In Scope

• Develop usage of Subject management service

• Develop usage of Subject registration service

• Out of Scope

• None

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2.1.9.2 Integrate with PSC – Out of Scope

• Will be discussed in the upcoming Code Jamboree

• caTissue architecture to achieve PSC integration

• Resolution of domain model differences

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2.1.10 Structured Specimen Protocols

• In Scope

• Develop Structured Specimen Protocols

• Need to iterate with NCI on data structure of protocols

• Will need input from community

• Structured protocol application data made available via the API and

caGrid services.

• Out of Scope

• None

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2.1.10.1 Integrate with Biospecimen Research Database

• In Scope

• Integrate with Biospecimen Research Database (BRD) via XMI file

exchange

• Specimen protocol application data including events, event

parameters, and ordering exposed via caCORE-like API and caGrid

service

• Out of Scope

• Import Specimen protocols from BRD

• Writable APIs for protocol creation

• caTissue UI-based integration with BRD

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2.1.11 Implement Common Biorepository Model

• In Scope

• Sharing of summary caTissue data via Common Biorepository Model

• Implemented by supplemental collection protocol data provided by

spreadsheet

• Out of Scope

• caTissue UI entry of supplemental collection protocol data

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2.1.12 API and Grid Service

• In Scope

• Integrate with Grid Grouper to allow users and groups to be

provisioned across institutional boundaries

• Out of Scope

• None

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Opportunities for involvement

• Feedback on demos and requirements• Hands on Testing

• On the demo site where possible• Locally where necessary

• Code Jamboree

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caTissue Suite 2.0 - Ready for feedback

• On 2.0 demo site• http://catissuesuitea.wustl.edu/catissuecore • MAGE-Tab export• caGrid User logon migration process

• Local install• Carry out revised build

• Requirements feedbackhttps://cabig-kc.nci.nih.gov/Biospecimen/KC/index.php/

CaTissue2.0dev

caBIG® Tissue Banks and Pathology Tools

caTissue Suite Code Jamboree

(Week of June 20 or

June 27)

Code Jamboree

• As we develop caTissue Suite 2.0 we will be reviewing its code architecture.

• Primary Goal• Make it easier for the community to make

their own code modifications• Secondary Goal

• Contribute the code back for use by others. • An opportunity to gather re-factoring input

and recommendations from the Tissue Banking Community

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Technical caTissue Suite Community Participation

• Installed sites• Developers from sites using caTissue Suite to

manage biospecimens• Support Service Providers• caTissue Suite funded developers • NCI TBPT program management

• Contractor supported

Whom Should Attend?• Those that have used caTissue and have tried to

extend it via• Modifying the source code• Writing extensions to the known hooks

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Overview of Code Jamboree

• Multi-day working session (3-4 days)

• Code review and/or code re-organization

• Open call for participants • Email fernandez_anna@bah.com or

digiulian_beth@bah.com • TBPT will be to ensure attendees have

sufficient background with caTissue to be effective

• Sessions will be structured to accommodate demand

Logistics

Date: Week of June 20 or June 27, 2011

Venue: TBD

Breakout sessions

Length: 2 – 4 days (TBD)

Time: 8:30am to 5 PM.

Hotel: Near Venue

Expected number of Attendees: ~20

Logistics• Date: Week of June

20 or June 27, 2011• Venue: TBD• Breakout sessions• Length: 2 – 4 days

(TBD)• Time: 8:30am to 5

PM.• Hotel: Near Venue • Expected number of

Attendees: ~20

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Goals

• Detail method to develop/revise code architecture for modularization of caTissue Suite 2.0 • framework that will allow for neutral “hooks” where local

code can be connected. • Detail method and develop/revise code for improving specific

functionality in caTissue Suite including but not limited to:• Dynamic extensions• Label generation• Printer integration• Barcode integration• Use of the APIs• Use of the grid service – programmatically• How to improve access to standards vocabularies and more

easily incorporate them in customization

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Long term commitment

• Those that volunteer for this working week of discussions should also expect to participate in future design and code review sessions

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Fall 2011 Training Sessions

• June caTissue Code Jamboree is not for training in caTissue Suite

End-user and Technical Training Sessions• Fall 2011 caTissue Suite Users Meeting (Oct or Nov

2011) - TBD

• Will be combined with TBPT F2F

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Questions and Answers