caTissue Suite 2.0 Scope Detail TBPT Workspace call May 23, 2011

2 Agenda Introduction Review of detail of caTissue scope Opportunities for involvement caTissue Suite code jamboree Questions and Answers

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

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

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

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

7 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 Biospecimen Identifier In Scope Develop specs for Global Specimen Identifier Develop Global Specimen Identifier Service Host the Service at NCI

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.

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

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

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

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

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

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

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

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

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

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

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

20 Opportunities for involvement Feedback on demos and requirements Hands on Testing On the demo site where possible Locally where necessary Code Jamboree

21 caTissue Suite Ready for feedback On 2.0 demo site MAGE-Tab export caGrid User logon migration process Local install Carry out revised build Requirements feedback 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

24 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

25 Overview of Code Jamboree Multi-day working session (3-4 days) Code review and/or code re- organization Open call for participants or 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

26 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

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

28 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

29 Questions and Answers