AMIALabKey2014V23

Report
LabKey Server
The Open Source Platform
for Large-Scale, Translational Research
April 10, 2014
AMIA Joint Summits – CRI Conference
Elizabeth Nelson, PhD
Scientific Outreach Director, LabKey Software
[email protected]
Continuing Education
 Disclosures
 I am an employee of LabKey Software, a for-profit entity
 LabKey Software consults for many not-for-profit and forprofit organizations
 LabKey Software supports and extends LabKey Server
 Learning Objectives
 After participating in this activity, the learner should be
able to explain why a research organization would need a
tool like LabKey Server and describe several use cases
Collaborators/Users
Fred Hutchinson Cancer
Research Center (FHCRC)
Statistical Center for HIV/AIDS
Research and Prevention (SCHARP)
NWBioTrust
City of Hope
Network for Pancreatic
Organ Donors (nPOD)
University of
Washington
Seattle Children’s Research
Institute (SCRI)
Center for HIV-AIDS Vaccine
Immunology (CHAVI)
University of
Wisconsin
Stanford
University
TB Systems Biology (TBSB)
Collaboration
Center for Modeling Immunity to
Enteric Pathogens (MIEP)
Pharmaceutical companies
Collaboration for AIDS
Vaccine Discovery (CAVD)
Wisconsin National Primate
Research Center (WNPRC)
Human Immunology Project
Consortium (HIPC)
HIV Prevention Trials
Network (HPTN)
Immune Tolerance
Network (ITN)
HIV Vaccine Trials
Network (HVTN)
Microbial Trials Network
(MTN)
Benaroya Research
Institute
Oregon National Primate
Research Center (ONPRC)
University Hospital of
Bern, Switzerland
Infectious Disease
Research Institute (IDRI)
University of Rochester
Medical Center (URMC)
Duke University
University of
Southern California
Virginia Tech
Harvard
University
International Center for Excellence
in Malaria Research (ICEMR)
Rho
University of New South Wales, Case Western
Australia
Reserve University
University of Kentucky, Markey
Cancer Center
University of California, Los Angeles
DF/Net Research
Data Challenges
 Variety
 Clinical, specimen, assay
 Annotations, metadata, provenance
 Variability
 Non-standard reporting
 Veracity
 Replication, validation, auditing
 Volume
 1000s of high-throughput runs
 100s of millions of results
 Velocity of arrival
 Velocity of change
 Evolving, complex analyses
 Virtuous cycles
 Hypothesis generation
 Ancillary studies
 Virtual teams
 Distributed, specialized
 Data silos
Solutions – Processes Plus Tools
Clinical Sites
ID
Weight
CD4+
Viral Load
Cell #
2496
142
420
12.2
163
2407
167
344
13.2
163
2427
112
897
21.0
161
Labs
Specimen
Repositories
Results
Study1
Study2
Study3
QC
Analysis
Manuscript
LabKey Server Stats
 Open Source
 No license fees, free to download, Apache 2.0
 http://labkey.org
 Proven, supported
 First release: 2005
 Active installations: 100+
Investments: $20 million+
3 Illustrative Stories
1. Operations and insight
2. Post-publication sharing
3. Cross-study hypothesis generation
Example 1: Atlas Science Portal
Statistical Center for HIV/AIDS Research and Prevention (SCHARP) at FHCRC
http://atlas.scharp.org
Nelson et al., BMC
Bioinformatics 2011
Atlas: Needs

Get better data – Facilitate annotation, standardization,
QC, and review during data acquisition

Get the full picture - Bring together different types and
source of information to learn more

Collaborate – Leverage distributed perspectives and
expertise
Atlas: Data Integration Nexus
Clinical
Records
Assay Data
& Metadata
Specimen
Information
Atlas: Data Integration Nexus
Clinical
Records
DataFax - SAS
Assay Data
& Metadata
Specimen
Information
LIMS
LIMS
LIMS
Atlas: Visualization, Analysis, Export
Atlas: Results
In production use since 2005 (9 years)
 Thousands of users across multiple consortia
 10s of thousands of assay runs
 Over a million vial transfers

Atlas: Results
RV-144
+/-
3 Stories
1. Operations and insight
2. Post-publication sharing
3. Cross-study hypothesis generation
Example 2: ITN TrialShare
Immune Tolerance Network (ITN)
http://itntrialshare.org
ITN TrialShare: Needs

Everything Atlas required, plus…

Transparency and reproducibility - Enable public
validation and extension of clinical trial findings

De-identification – Ensure participant confidentiality
ITN TrialShare: First Publication
Specks et al., NEJM 2013
ITN TrialShare: Interactive Figures
ITN TrialShare: Manuscript Figures with Analysis Code
Original
Analysis
Data
Userdefined
Filters
Code
ITN TrialShare: Results

20 clinical trials
Terabytes of information
 3,200 patients
 72,000 study visits
 700 users

http://trialshare.org
3 Stories
1. Operations and insight
2. Post-publication sharing
3. Cross-study hypothesis generation
Example 3: HIV Vaccine Collaborative Dataspace
Statistical Center for HIV/AIDS Research and Prevention (SCHARP) at FHCRC
Dataspace: Needs

Wider collaboration – Pool data and expertise across
the wider HIV vaccine research community

Cross-study hypothesis generation – Make the most
of existing data and past funding
Dataspace
Dataspace
Dataspace
Dataspace
Dataspace
Dataspace
Dataspace
Dataspace
Dataspace
PLOT UPDATED HERE
ADDED FILTER
HERE
Dataspace
PLOT UPDATED HERE
ADDED FILTER
HERE
Dataspace
ADDED FILTER
HERE
Future: Hutch Integrated Data Repository Archive (HIDRA)
Thanks!
http://labkey.org
 LabKey team
 Many, many
collaborators











FHCRC
SCHARP
HVTN
CAVD
Duke
UW
ITN
Artefact
NIH
JDRF
Bill & Melinda
Gates Foundation…
NIH Credit/Disclaimer:
 Research reported in this talk was supported by the
National Institutes of Health
 The content of this talk is solely the responsibility of
the authors and does not necessarily represent the
official views of the National Institutes of Health
Thanks!
Fred Hutchinson Cancer
Research Center (FHCRC)
Statistical Center for HIV/AIDS
Research and Prevention (SCHARP)
NWBioTrust
City of Hope
Network for Pancreatic
Organ Donors (nPOD)
University of
Washington
Seattle Children’s Research
Institute (SCRI)
Center for HIV-AIDS Vaccine
Immunology (CHAVI)
University of
Wisconsin
Stanford
University
TB Systems Biology (TBSB)
Collaboration
Center for Modeling Immunity to
Enteric Pathogens (MIEP)
Pharmaceutical companies
Collaboration for AIDS
Vaccine Discovery (CAVD)
Wisconsin National Primate
Research Center (WNPRC)
Human Immunology Project
Consortium (HIPC)
HIV Prevention Trials
Network (HPTN)
Immune Tolerance
Network (ITN)
HIV Vaccine Trials
Network (HVTN)
Microbial Trials Network
(MTN)
Benaroya Research
Institute
Oregon National Primate
Research Center (ONPRC)
University Hospital of
Bern, Switzerland
Infectious Disease
Research Institute (IDRI)
University of Rochester
Medical Center (URMC)
Duke University
University of
Southern California
Virginia Tech
Harvard
University
International Center for Excellence
in Malaria Research (ICEMR)
Rho
University of New South Wales, Case Western
Australia
Reserve University
University of Kentucky, Markey
Cancer Center
University of California, Los Angeles
DF/Net Research
Elizabeth Nelson
[email protected]
Questions?

Extra slides
Where Does LabKey Server Fit?
Spotfire
Analysis, visualization, reporting
Freezerworks
Sharepoint
LIMS - specimen tracking
Instruments
Data processing
REDCap
Data capture
Collaboration
Integration
Collaboration
Standardization
Exploration
i2b2
Cohort discovery
tranSMART
Data mining
Where Does LabKey Server Fit?
(Image from Embi & Payne, JAMIA 2009)
Customization and Extension
LabKey Server
Labkey
File System 2
SAS Share
File System
LabKey Database
(PostgreSQL or
MS SQL)
Data 1
LabKey Schemas
Data 2
External
Schemas
Oracle
MS SQL
Database
My SQL

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