Expanding Access to OpenClinica Data via LabKey Server Peter Hussey 2013 OpenClinica Global Conference Founding Partner, LabKey Software June 21, 2013

 Volume  Terabytes of raw data from molecular and cellular assays  Velocity  High throughput assays for more and larger studies  Variety  Combine clinical and lab assays across labs & systems Data challenges for research networks & labs  Veracity  Quality, consistency, reproducibility, provenance  Value  Secure and sharable across research teams and studies ing spreadsheets isn’t going to cut it anymore

 Open source platform for data integration and collaboration  Target users: research networks and labs doing translational studies  Proven infrastructure  First release: 2005  Investment in the platform to date: $15+ million  Active installations: 100+  Professionally supported by LabKey Software LabKey Server ITN TrialShare

a ta CRF Data LabKey Server for Data Integration Clinical Site(s) Integrated results, reports, and analysis Discoveries, Publications, Hypotheses, Proposals LabKey Server Lab(s) LIMS Assay Data Results Open Clinica

Support for Complex Lab Assay Data Clinical Site(s) Integrated results, reports, and analysis Discoveries, Publications, Hypotheses, Proposals LabKey Server Open Clinica Lab(s) LIMS Assay Data Results

6 Assay data upload example

7

8 Piehler et al., BMC Immunology 2011 Neutralizing Antibody

…. and more assay data Shulman et al., Cytometry 2008 Flow Cytometry

…. and more assay data Eckels et al., BMC Bioinformatics 2013 Luminex ®

a ta CRF Data LabKey Server for Data Integration Clinical Site(s) Integrated results, reports, and analysis Discoveries, Publications, Hypotheses, Proposals LabKey Server Lab(s) LIMS Assay Data Results Open Clinica

LabKey Study: Site of Data Integration LabKey Server Lab #2 Folder (Private) Integrated Data View Clinical Results Demographics Neutralizing Antibody Dataset Lab #1 Folder (Private) Specimen Information LIMS #1 External Data Sources LIMS #2 Neutralizing Antibody Assay Runs Open Clinica Luminex Assay Runs Luminex Dataset Study Folder (Shared)

Data integration 13 Participant IDDateResultAnalyte A11/13/ IFN-a A11/13/ IL-2 A11/20/ IFN-a A11/20/ IL-2 B6/13/ IL-2 B6/20/ IL-2 GenderEnroll Date Male11/1/2001 Male11/1/2001 Male11/1/2001 Male11/1/2001 Female6/1/2012 Female6/1/2012 Weight Days since enroll Assay resultsDemographicsCalculated Clinical results

14 Visualization of cohort results

Platform extension and customization Labkey File System 2SAS Share Data 1 Data 2 File System LabKey Database (PostgreSQL, MS SQL) LabKey Schemas More Schemas OpenClinicaOracleMy SQL LabKey Server

Explore analyses in R

Collaborators/funders include… Organizations & Networks  Immune Tolerance Network (ITN)  HIV Vaccine Trial Network (HVTN) and other HIV networks (MTN, HPTN, …)  Fred Hutchinson Cancer Research Center (FHCRC)  Statistical Center for HIV/AIDS Research and Prevention (SCHARP)  Center for HIV-AIDS Vaccine Immunology (CHAVI)  Collaboration for AIDS Vaccine Discovery (CAVD)  Human Immunology Project Consortium (HIPC)  Wisconsin National Primate Research Center (WNPRC)  Oregon National Primate Research Center (ONPRC)  Juvenile Diabetes Research Foundation Network for Pancreatic Organ Donors (nPOD)  University of Washington International Center for Excellence in Malaria Research (ICEMR)  NWBioTrust  TB Systems Biology (TBSB) collaboration  LabKey Software team  … Labs  Katze (UW)  Kiem (FHCRC)  Letvin (Harvard)  MacCoss (UW)  Mallick (USC)  McElrath/DeRosa (FHCRC)  McIntosh (FHCRC)  Montefiori (Duke)  O’Connor (Wisconsin)  Tomaras (Duke)  … 17 Research reported in this talk was supported by the National Institutes of Health under award numbers UM1- AI , U01-AI , and many others.

Reference materials  Documentation, tutorials, videos, forums, installers   Overview paper  Nelson et al., LabKey Server: An open source platform for scientific data integration, analysis and collaboration. BMC Bioinformatics 2011LabKey Server: An open source platform for scientific data integration, analysis and collaboration  2013 User Conference  Seattle, September th   Training, tips, user presentations NIH Disclaimer: 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

Questions? Peter Hussey