open source, open data, & personalized medicine Benaroya - PowerPoint PPT Presentation

open source, open data, & personalized medicine Benaroya Research Institute

open source & open data

Agenda a little about the Benaroya Research Institute what is personalized medicine? the project data collection analysis dissemination making our work (and tools) public

Benaroya Research Institute Benaroya Research Institute at Virginia Mason is located in Seattle 220 scientists and staff primarily focused on finding the causes and cures for autoimmune diseases 5 Core Laboratories 15 Laboratories 100 clinical trials enrolling patients at any time

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Systems Immunology GENOMICS CORE SYSTEMS IMMUNOLOGY BIOINFORMATICS BIOSTATISTICS SOFTWARE DEV.

Personalized Medicine

starting with just

healthy

not so healthy...

technology platforms

processing the results CHAUSSABEL ET AL. IMMUNITY 2008

query the reference DB

disease progression CHAUSSABEL ET AL. IMMUNITY 2008

understanding disease

category B pathogens

clinical data & sample collection logistics storing samples shipping samples access to computers language (i18n) naming conventions

case report forms

HTTPS://WWW.OPENCLINICA.COM/

HTTP://WWW.PROJECT-REDCAP.ORG/

adding in experimental data genomics microarray NanoString rna-Seq flow cytometry luminex RT PCR ELISPOT etc

adding in experimental data custom systems LabKey

HTTPS://WWW.LABKEY.ORG/

Browsing the data together

Browsing the data together

more data (cross project)

getting more data collaborators (sharing between friends) NCBI GEO Array Express IMMPORT Supplemental Materials & Email

open data

OPEN != ACCESSIBLE

OPEN != USEABLE

CURATION SCIENTIST

finding & open data

where are we?

making it available Access through different science portals Immune Tolerance Network Cooperative Center for Human Immunology Systems Immunology at Benaroya Research Publications Interactive Figures Downloadable supplemental results

making the data accessible

publications Modules (Chaussabel et al, Immunity 2008, http:// www.ncbi.nlm.nih.gov/pmc/articles/ PMC2727981/?tool=pubmed) Data Management (Chaussabel et al, Nature Immunology 2009, http://www.ncbi.nlm.nih.gov/ pmc/articles/PMC2788787/?tool=pubmed) Signature in Tuberculosis (Berry et al., Nature, 2010)

publications pending Modules Gene Expression Browser Knowledge Management

Acknowledgements & Thanks Immune Tolerance Network (http:// immunetolerance.org/) Atul Butte Lab, Stanford University (http:// buttelab.stanford.edu/) Cooperative Center for Human Immunology (http://www.humanimmunology.org/)

thank you to the developers

For more information... cquinn@benaroyaresearch.org