Secure Data Management in BIRN. Karl Helmer Massachusetts General Hospital September 6, 2011 For the BIRN Consortium. Talk Outline:. BIRN Overview Data Services Overview Example Use Cases: -Function BIRN (FBIRN) Data Federation -Pathology Viewer Project Working with BIRN.
Massachusetts General Hospital
September 6, 2011
For the BIRN Consortium
-Function BIRN (FBIRN) Data Federation
-Pathology Viewer Project
“to advance biomedical research through data sharing and online collaboration”
What is the main challenges of collaborative science?
The challenge is heterogeneity in both:
BIRN is driven by the things our users want
Develop Capabilities – i.e., our ability to:
Multisite Study of Schizophrenia
Ozyurt, Keator, et. al. Neuroinformatics. 2010 Dec;8(4):231-49.
Automated image upload to Data Grid/HID for sharing (DICOM -> NIfTI)
Result Images and XML wrapper in Data Grid
(FIPS, SPM, FreeSurfer,etc)
Results with standard descriptions in HID (i.e. data provenance)
Computer aided scale input via clinical data entry interface and remote tablet PC interface
Multi-Site User Query
Keator, et. al. IEEE Trans Inf Technol Biomed. 2008 Mar;12(2):162-72.
Adjust to user and project preferences, relax for > performance
Fewer vulnerabilities for data security
Collaborative project data sharing
Improve small file transfer performance
Improve large file transfer performance
The BIRN Pathology project began in early 2010
Objective was to create a new shared resource for the research community: an online collection of pathology data, including very high resolution microscopy images
Initial user group consists of pathologists
ISI developing the infrastructure
Early phases: rapid prototyping and iteration with users to build out the core data model, user workflows and user experience, and investigation of microscopy tools
January 2011: packaged (RPM), documented (wiki), released (YUM repo) the version 1.0 of the system
Ongoing enhancements to data model, microscopy image support, refactoring of system into reusable components
Application (e.g., Pathology)
Other BIRN “Capabilities”
3rd Party Tools
Scientists need to create custom web-accessible databases to share data within and between research groups.
Scientists store data on spreadsheets, need to manage this data (DBMS), and expose it programmatically (WS REST)
Scientists need to share high resolution (100X) images over relatively low bandwidth networks.
Scientists need to annotate and share annotations on images.
Scientists need to search their databases using full-text queries and field-based “advanced” search queries.
Pathologists create images in proprietary microscopy formats, annotate the images, and need to upload them to a web-accessible database for sharing among collaborating sites.
Pathologists associate metadata and supplementary files with their microscopy images.
IvoDinov, Fabio Macciardi, Federica Torri, Jim Knowles, Andy Clark, Joe Ames, Carl Kesselman, and Arthur Toga
Next Generation Sequence Analysis
Pipeline Web-Start (PWS)http://pipeline.loni.ucla.edu/PWS
Community Pipeline Workflowshttp://www.MyExperiment.org/workflows
Email address: [email protected]
Joe Ames: [email protected]
Karl Helmer:[email protected]
BIRN is supported by NCRR and NIH grants 1U24-RR025736, U24-RR021992, U24-RR021760 and by the Collaborative Tools Support Network Award 1U24-RR026057-01.