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?