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 for profit 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) HIV Vaccine Trials Network (HVTN) Immune Tolerance Network (ITN) Collaboration for AIDS Vaccine Discovery (CAVD) Statistical Center for HIV/AIDS Research and Prevention (SCHARP) NWBioTrust City of Hope Seattle Children’s Research Institute (SCRI) Human Immunology Project Consortium (HIPC) Center for HIV-AIDS Vaccine Immunology (CHAVI) HIV Prevention Trials Network (HPTN) TB Systems Biology (TBSB) Collaboration Center for Modeling Immunity to Enteric Pathogens (MIEP) Pharmaceutical companies University of Washington University of Wisconsin Stanford University Wisconsin National Primate Research Center (WNPRC) Oregon National Primate Research Center (ONPRC) Network for Pancreatic Organ Donors (nPOD) University Hospital of Bern, Switzerland Benaroya Research Institute Infectious Disease Research Institute (IDRI) University of Southern California Virginia Tech University of Rochester Medical Center (URMC) Duke University Harvard University Microbial Trials Network (MTN) International Center for Excellence in Malaria Research (ICEMR) Rho University of New South Wales, Australia Case Western 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

2496 2407 2427

Weight

142 167 112

CD4+

420 344 897

Viral Load

12.2

13.2

21.0

Cell #

163 163 161

Labs Specimen Repositories

Study1 Results 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 Assay Data & Metadata DataFax - SAS Specimen Information

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

Data Original Analysis User defined 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!

  LabKey team Many, many collaborators  FHCRC  SCHARP  HVTN  CAVD  Duke  UW  ITN  Artefact  NIH  JDRF  Bill & Melinda Gates Foundation… http://labkey.org

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) HIV Vaccine Trials Network (HVTN) Immune Tolerance Network (ITN) Collaboration for AIDS Vaccine Discovery (CAVD) Statistical Center for HIV/AIDS Research and Prevention (SCHARP) NWBioTrust City of Hope Seattle Children’s Research Institute (SCRI) Human Immunology Project Consortium (HIPC) Center for HIV-AIDS Vaccine Immunology (CHAVI) HIV Prevention Trials Network (HPTN) TB Systems Biology (TBSB) Collaboration Center for Modeling Immunity to Enteric Pathogens (MIEP) Pharmaceutical companies University of Washington University of Wisconsin Stanford University Wisconsin National Primate Research Center (WNPRC) Oregon National Primate Research Center (ONPRC) Network for Pancreatic Organ Donors (nPOD) University Hospital of Bern, Switzerland Benaroya Research Institute Infectious Disease Research Institute (IDRI) University of Southern California Virginia Tech University of Rochester Medical Center (URMC) Duke University Harvard University Microbial Trials Network (MTN) International Center for Excellence in Malaria Research (ICEMR) Rho University of New South Wales, Australia Case Western 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?

Freezerworks

LIMS - specimen tracking

Instruments

Data processing

Spotfire

Analysis, visualization, reporting

Sharepoint

Collaboration Integration Collaboration Standardization Exploration

i2b2

Cohort discovery

REDCap

Data capture

tranSMART

Data mining

Where Does LabKey Server Fit?

(Image from Embi & Payne, JAMIA 2009)

Customization and Extension File System 2 SAS Share Data 1

LabKey Server

Labkey File System LabKey Database (PostgreSQL or MS SQL) LabKey Schemas Oracle Data 2 External Schemas MS SQL Database My SQL