caTissue Future

1 Feb 2013

Ian Fore, Juli Klemm, Lisa Mahoney, Jose Galvez & Cliff Wong

Outline

• Introduction & NCIP• Status/release of caTissue 2.0• Revised support mechanisms• NCI funded development of caTissue• Open development• Code Jamboree 2• User group meetings• Discussion• Summary

National Cancer Informatics Program

• Announced by Dr Harold Varmus, Director of NCI– April 2012

• NCIP Blog– http://ncip.nci.nih.gov/blog

• Twitter– @NCI_NCIP

• LinkedIn Group– NCIP - National Cancer Informatics Program

caTissue as a product - Three levels

• A product for use by end users– Web application

• A product for use by system integrators– Application Programmers Interface

• An open source product for customization by coders– Source code

caTissue Suite 2.0 - Thanks• NCI management

– Cliff Wong, Sichen Liu

• Development managed by SAIC-Frederick– Sreenath Nampally

• Development work by– Washington University in St Louis– Krishagni– Semantic Bits

• Contracted requirements and testing– Thomas Jefferson University– Emory University– Yale University

• Biospecimen Informatics Program Management– Booz Allen Hamiliton– Anna Fernandez, Beth DiGiulian, Lynn Martin

• caTissue user and developer community– Community Coders tested new build process - gratis

caTissue Suite 2.0 features – end user

• Ability to manage and represent Specimen Processing Procedures (SPPs) associated with individual collection protocols

• Use unique identifiers across organizations• Ability to store and query age at collection• Bulk operation enhancements • Interoperability with assay systems such as caArray via

MAGE-TAB files• Integration with the NCI Clinical Trials Report Program

(CTRP) data sources for person, organization, and studies• Integration with patient registrations applications (e.g. C3PR)• Publish summary information via CBM• Many legacy bug fixes

caTissue Suite 2.0 features - technical

• Support for caGrid-based authentication and authorization in the Web application and caGrid API

• Single caGrid data service simplifies both "static" model and dynamic extension queries

• caGrid service now a full read-write biospecimen service• Improved source code organization and build process

that uses NCI Build and Deployment Automation (BDA) framework

• Many security issues addressed

Security Vulnerabilities in caTissue

• 73% of organizations have been hacked at least once in the past two years through insecure Web applications.1  

• 70% of threats occur with the application.2  – As opposed to the server or other infrastructure

• NIH/NCI use a commercial web application scanner to search for vulnerabilities.

• A scan of caTissue 2.0 found a number of vulnerabilities that need remediation.

• The vulnerabilities are currently being addressed and testing is scheduled to complete in Feb. 2013

1. State of Web Application Security Survey, Ponemon Institute

2. Gartner Research

Status/release of caTissue 2.0• There remain some testing issues which are being

resolved• Security vulnerability• Common Biorepository model export issues

• Release of caTissue Suite 2.0 will generate a need for support– Some compromises in the new release

caTissue Support

• Prior Support Mechanism– Knowledge Center - Closed May 2012– Forums – active

• NCIP Application support– Phone: 240-276-5541– Email: ncicbiit@mail.nih.gov

• Community driven Support– Community support experts

• Community individuals supported by CBIIT as caTissue experts– Answer community questions from the listserve and forums– Create and maintain knowledge on the Wiki site

– caTissue Wiki• https://wiki.nci.nih.gov/display/TBPTKC/Tissue-Biospecimen+Bankin

g+and+Technology+Tools+Knowledge+Center

– Forums• https://cabig-kc.nci.nih.gov/Biospecimen/forums/

Knowledge Center forums remain active

2013 NCI funded development of caTissue• NCI is working on doing some development through an

appropriate mechanism• Main objective

– Increase suitability for development and contributions by a broad community

– Engineering oversight will come from within NCI

• Expected to commence in second quarter 2013

Open development of caTissue• Under NCIP Open Development Initiative

– http://ncip.nci.nih.gov/blog/tag/open-development/

• NCIP GitHub– https://github.com/ncip

• Continue the strong line of caTissue open development

Center Name Center Name Center Name

Washington Univ Louisiana Cancer Research Consortium

Christiana Health Care Systems

Indiana Univ John Hopkins Univ. Emory Univ.

Dana Farber Cancer Institute

Accelerated Community Oncology Research Network

Univ. of Edinburgh

Loma Linda Univ. Ohio State Univ. Univ. of Nebraska

Huntsman Cancer Institute

University of California, Davis

Vrije Universiteit, Amsterdam

Yale Univ. Univ. of Michigan C-DAC, Pune

Washington UnivLouisiana Cancer Research ConsortiumChristiana Health Care SystemsIndiana UnivJohn Hopkins Univ.Emory Univ.Dana Farber Cancer InstituteAccelerated Community Oncology Research NetworkUniv. of EdinburghLoma Linda Univ.Ohio State Univ.Univ. of Nebraska Huntsman Cancer Institute University of California, DavisYale Univ.Univ. of MichigancaTissue Suite Community Development

Examples of recent community development

• Krishagni– caTissue Plus

• Vrije (Free) Universiteit – Amsterdam– Modifications to CBM export

Governance

• How will the future direction of caTissue be set?

• Establish a governance team– Not a single institution or company– An evolution of the caTissue Community Code group

• Identify community leadership for that group

• caLIMS 2 is already doing something similar– Some different considerations apply for caTissue

caTissue within NCIP

• NCI’s continuing interest includes– caTissue as a tool to improve biospecimen management and

support best practices– caTissue as an interoperable application

• To enable cross disciplinary and cross institutional research

• Interoperability - the past– caTissue dynamic extensions is a unique example of the

integration of an application with the caBIG infrastructure

• Interoperability - the future– Wish to see that continue as NCIP moves to

• Revised semantic infrastructure• Revised interoperability framework

– E.g. Make easier what was done by the Prostate SPOREs

Some mechanics

• Migration of caBIG source code to GitHub– From Subversion at NCI

• Timing to be determined for caTissue• Opportunity for revising code modularization

– Again!

• Issues to be addressed by the community code group

Community Code teleconference

• Items up for the agenda– SVN check in

• Review of request mechanism

– GitHub migration– caTissue Plus code management

• Krishagni

– CBM ETL revisions• Vrije Universiteit Amsterdam

– Security fixes• SAIC team

• Please make other suggestions

The Code Jamboree

• It’s about the code– i.e. the third level

• It’s about the situations where…– There wasn’t enough money– There wasn’t enough time– We didn’t think about it– We got it “wrong”

…and you want to change the code yourself

• Code Jamboree 2• In planning for 2013

User group meetings• Goal

– Learning about caTissue– Provide user feedback

• Program committee (as in 2011)– Drawn from users– Biobankers!

• Material– From the user community– Community Support Experts

• Location– To be determined

Putting the above together

• Community development alongside NCI development• Jamboree and code community calls

– Parallel threads of continued activity

Future meetings

• Biospecimen Informatics calls– Monthly

• User Group meeting– Annual

• Community code contributions– Monthly

• caTissue Code Jamboree– Annual/biannual

Discussion – the floor is yours

• But some possible topics…

• Some sites will not be comfortable with open source– Sceptical IT departments?– How can we help?

• How much does application security matter to you?• Thoughts about revised support mechanisms• Level of interest in code Jamboree • Level of interest in User Group Meeting• Other concerns/questions?

• This call is recorded unless you object– Please say so

Summary of links

• caTissue– Wiki

• https://wiki.nci.nih.gov/display/TBPTKC/Tissue-Biospecimen+Banking+and+Technology+Tools+Knowledge+Center

– Forums• https://cabig-kc.nci.nih.gov/Biospecimen/forums/

– NCIP Application support• Phone: 240-276-5541• Email: ncicbiit@mail.nih.gov

• National Cancer Informatics Program– NCIP Blog

• http://ncip.nci.nih.gov/blog

– Twitter• @NCI_NCIP

– LinkedIn Group– NCIP - National Cancer Informatics Program