OpenSpecimen Adoption and Integration at Washington University School of Medicine St. Louis, MO.
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Transcript of OpenSpecimen Adoption and Integration at Washington University School of Medicine St. Louis, MO.
OpenSpecimen Adoption and Integration at Washington University School of Medicine
St. Louis, MO
IT infrastructure Supporting local users
Testing Training
Informatics Integration Points
Topics Covered
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
IT Infrastructure
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
Monitoring and Availability
Virtualization
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
Databases
Application Server (JBoss) Web Server
Operating System Version CentOS 6.5 CentOS 6.5
Local Disk Space 16GB 16GB
Mounted Disk Space 25GB NA
RAM 8GB 1GB
Number of Cores 2 1
JBoss Version 5.1 NA
Ant Version 1.7 NA
Java Version 1.6.0.31 NA
Apache Version NA 2.2
OpenSpecimen Server Specs
IT infrastructure Supporting local users
Testing Training
Informatics Integration Points
Topics Covered
Release Timeline
StartMon 1/2/06
FinishMon 3/2/15
August 11 August 21 September 1 September 11 September 21 October 1 October 11 October 21 November 1NCI Funded Development
Mon 1/2/06 - Mon 9/30/13
Community Funded Development Thu 1/12/12 - Mon 3/2/15
caTissue Core 1.0Mon 1/2/06
caTissue Core 1.2Mon 5/21/07
caTissue Suite 1.0Thu 4/10/08
caTissue Suite 1.1Wed 2/18/09
caTissue Suite 1.1.1Tue 11/10/09
caTissue Suite 1.1.2Fri 1/29/10
caTissue Suite 1.2Fri 3/18/11
caTissue Plus 1.0Thu 11/1/12
caTissue Plus 2.0Fri 2/1/13
caTissue Plus 3.0Thu 8/1/13
caTissue Suite 2.0Mon 9/30/13
caTissue Plus 3.1Wed 1/1/14
caTissue Plus 3.2Sun 3/2/14
OpenSpecimen 1.0Mon 6/2/14
caTissue Plus 3.2.1Fri 7/11/14
OpenSpecimen 2.0Mon 12/1/14
OpenSpecimen 3.0Mon 3/2/15
WashU LTP goes live with Core 1.2
Users n=5
• Alzheimer Disease • Renal Research• Hepatobiliary – Pancreas • Gut Microbiome• Pulmonary
Users n=100
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.
Governance
Kris
hagn
i Sol
ution
s
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
Input from Adopters
Development Quality Assurance Production
Migration Mechanism
• Proof of Concept• Feature Verification• Functional and Regression Testing• Integration and Load Testing
Data Update Data Update
Application Update Application Update
• User Documentation and Training• Quality Testing • Full Integration Testing
• End User Upgrade Notification • Application Support• Requirement / Feature Documentation
Data 2~4 weeks old Data 1~2 days old
Around 6 releases per year(high impact / low effort)
Local customizations 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
Challenges
Most heavy on CBMI 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
Testing
Atlassian – Confluence and JIRA
Documentaion
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 https://cabigtrainingdocs.nci.nih.gov/caTissuePortal/index.html
Training
IT infrastructure Supporting local users
Testing Training
Informatics Integration Points
Topics Covered
ClinPortal Integration
ClinPortalData management caTissue
CIDERData
warehouse
*Lab resultsDemographicsMedicationsDiagnosis ProceduresAdmit/DC
Clinical Research at WUSM
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
ClinPortal-OpenSpecimen Integration
Participant
Clinical StudyRegistration
Collection ProtocolRegistration
Clinical Study Collection Protocol
CS Event CP Event
Visit SCG
Form 1Form 2
…
Specimen 1Specimen 2
…
ClinPortal caTissue*1
*2
Nagarajan Lab, 2012
ClinPortal-OpenSpecimen Integration
Nagarajan Lab, 2012
ClinPortal classes
caTissue classes
Join based on Participant Study ID
Integrated Query
ClinPortal-OpenSpecimen Integration
ClinPortal Event – Activate Encounter
No separate caTissue login action required
for navigation
Nagarajan Lab, 2012
ClinPortal-OpenSpecimen Integration
Nagarajan Lab, 2012
Electronic Master Patient Index
eMPIIntegration
Nagarajan Lab, 2012
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
WUSTL Biospecimen Navigator
Short term Development – Jan 2015 Deployment – March 2015
Long term Open source Biospecimen information management system
agnostic
WUSTL Biospecimen Navigator
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
Acknowledgements
Questions?