2. Topics Covered IT infrastructure Supporting local users
Testing
Training
Informatics Integration Points

3. IT Infrastructure
Currently all applications and web servers that are HIPAA compliant are located on the WUCON (Washington University Clinical Operations Network) behind two firewalls
External availability is provided through two load balanced MS Internet Security and Acceleration (ISA) servers to the internet

4. Monitoring and Availability
Currently setting up an HAProxy based Apache cloud in the DMZ to provide our own Named-based Virtual hosting into WUCON.
This will allow for unifying end to end responsibility, monitoring, and tracking
Not dependent on external (to CBMI) groups for support

5. Virtualization

6. Databases CBMI supports many different database for different projects
MySQL
MS SQL Server
DB2
PostgreSQL
For OpenSpecimen we currently use Oracle
Long term plans to move to PostgreSQL

7. OpenSpecimen Server Specs
Application Server (JBoss)
Web Server
Operating System Version
CentOS 6.5
Local Disk Space
16GB
Mounted Disk Space
25GB NA
RAM
8GB
1GB
Number of Cores 2 1
JBoss Version
5.1
Ant Version
1.7
Java Version
Apache Version
2.2

8. Topics Covered IT infrastructure Supporting local users
Testing
Training
Informatics Integration Points

9. Release Timeline Alzheimer Disease Renal Research
Start Mon 1/2/06
Finish Mon 3/2/15
August 11
August 21
September 1
September 11
September 21
October 1
October 11
October 21
November 1
NCI Funded Development Mon 1/2/06 - Mon 9/30/13
Community Funded Development Thu 1/12/12 - Mon 3/2/15
caTissue Core 1.0 Mon 1/2/06
caTissue Core 1.2 Mon 5/21/07
caTissue Suite 1.0 Thu 4/10/08
caTissue Suite 1.1 Wed 2/18/09
caTissue Suite Tue 11/10/09
caTissue Suite Fri 1/29/10
caTissue Suite 1.2 Fri 3/18/11
caTissue Plus 1.0 Thu 11/1/12
caTissue Plus 2.0 Fri 2/1/13
caTissue Plus 3.0 Thu 8/1/13
caTissue Suite 2.0 Mon 9/30/13
caTissue Plus 3.1 Wed 1/1/14
caTissue Plus 3.2 Sun 3/2/14
OpenSpecimen 1.0 Mon 6/2/14
caTissue Plus Fri 7/11/14
OpenSpecimen 2.0 Mon 12/1/14
OpenSpecimen 3.0 Mon 3/2/15
Alzheimer Disease
Renal Research
Hepatobiliary – Pancreas
Gut Microbiome
Pulmonary
Users n=100
WashU LTP goes
live with Core 1.2
Users n=5

10. Governance
A governance structure is in the process of being formalized
Current working form is similar to that of a benevolent dictator that has input from the OpenSpecimen community by way of adopters.
Input from Adopters
Krishagni Solutions
Adopter 1
Adopter 2
Adopter 3
Adopter n
Feature requests
Adopter funded development
New application version
New/more clients
Support
Goals:
Increase global adoption
Sustained funding model
Better product

11. Migration Mechanism Development Quality Assurance Production
Around 6 releases per year
Development
Quality Assurance
Production
(high impact / low effort)
Application Update
Application Update
Data 1~2 days old
Data 2~4 weeks old
Proof of Concept
Feature Verification
Functional and Regression Testing
Integration and Load Testing
End User Upgrade Notification
Application Support
Requirement / Feature Documentation
User Documentation and Training
Quality Testing
Full Integration Testing
Data Update
Data Update

12. Challenges Local customizations Enhancements Critical bug fixes BioMS
NCI Navigator
Data warehouse
ClinPortal (CDMS)
Enhancements
eMPI matching -> integration
Scroll bar disappears -> user interface
Critical bug fixes
JDBC connections not closed properly
PPI searches require data entered in exact order

13. Testing Most heavy on CBMI Limited end user testing
Test cases maintained in JIRA
Test plans tracked in JIRA
Can be >100 test cases depending on release
Limited end user testing
Push to engage more users
More users = more varied workflows

14. Documentaion
Atlassian – Confluence and JIRA

15. Training Monthly training for new users
Verification of HIPAA
2 hour long in-person session
Tailored training to users role
Online training via NCI e-Learning portal

16. Topics Covered IT infrastructure Supporting local users
Testing
Training
Informatics Integration Points

17. ClinPortal Integration
caTissue
ClinPortal
Data management
CIDER
Data warehouse
*Lab results
Demographics
Medications
Diagnosis
Procedures
Admit/DC
Clinical Research at WUSM

18. ClinPortal-OpenSpecimen Integration
Reduce redundancy in participant registry
“Simultaneous” registration in both systems
pending matching
Avoid duplicates in each system
Minimize data entry error
Navigation across systems
Single login
Additional method for querying participant data across systems
caTissue db ID stored as MRN in ClinPortal
Nagarajan Lab, 2012

19. ClinPortal-OpenSpecimen Integration
Participant
Clinical Study
Registration
Collection Protocol
Registration
ClinPortal
caTissue *1
Clinical Study
Collection Protocol *2
CS Event
CP Event
Register simultaneously
Visit
SCG
Form 1
Form 2 …
Specimen 1
Specimen 2 …
Nagarajan Lab, 2012 19

20. Join based on Participant Study ID
ClinPortal-OpenSpecimen Integration
Integrated Query
ClinPortal classes
Join based on Participant Study ID
caTissue classes
Nagarajan Lab, 2012

21. No separate caTissue login action required for navigation
ClinPortal-OpenSpecimen Integration
No separate caTissue login action required for navigation
ClinPortal Event – Activate Encounter
Nagarajan Lab, 2012

22. ClinPortal-OpenSpecimen Integration
Nagarajan Lab, 2012

23. eMPI
Integration
Electronic Master Patient Index
Nagarajan Lab, 2012

24. WUSTL Biospecimen Navigator
Goals
Simple UI for searching biospecimen inventory
Guest or WashU employee
Easily add or subtract from list
Submit biospecimen request with minimal data
Nice to have
End-to-end electronic workflow to support
Search
Request
Distribution
Billing

25. WUSTL Biospecimen Navigator
Short term
Development – Jan 2015
Deployment – March 2015
Long term
Open source
Biospecimen information management system agnostic

26. Acknowledgements The Center for Biomedical Informatics Leslie McIntosh
Mark Watson
Amy Brink
Snehil Gupta
Divya Khandekar
Melissa McKenna
Suhas Khot
Atul Kaushal
Bijoy George
Caerie Houchins
Keith Danderand
Megan Range

27. Questions?