community with rich web interfaces

feelingmomInternet and Web Development

Dec 7, 2013 (3 years and 6 months ago)

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Providing the cardiovascular
community with rich web interfaces
to integrate cardiovascular tools,
data and analysis

Stephen J. Granite, MS, MBA

CVRG Program Manager

NHLBI R24
-
HL085343

http://www.cvrgrid.org


Data Management Needs of the
Cardiovascular (CV) Community


CV
-
specific
ontologies

for describing data and data collection
protocols


Must address unique CV data types


Time
-
evolving

electrophysiology (EP), electrocardiogram (ECG), and
multi
-
modal image data


Software tools for managing diverse types of CV data


Must be well documented, easy to install/use, secure, and work
out of the box


Ability to query multiple data sources located and maintained
at different sites


Project design often requires that specific types of data be
collected and managed at different sites (e.g., MR Reading
Centers, ECG Reading Centers, etc)


The CVRG Project

Mission:

Serve the
needs of basic and clinical cardiovascular researchers
by providing seamless, customized, secure access to study
datasets and analysis
tools


Team:

Institute for Computational Medicine
, Johns Hopkins University (Winslow, Miller)

Image Lab
, Wake Forest University (Carr, Ge)

Center for Comprehensive Informatics
, Emory University (Saltz, Post)

Computation Institute
, University of Chicago (Foster,
Madduri
)

The CVRG Approach to

Technology Development


Don’t re
-
invent the wheel


When possible, re
-
use or extend software components from
National Center for Biomedical Computing (NCBC) & other open
-
source projects (e.g., i2b2,
Globus

Online, etc.)


Form collaborations to develop new software components


Address the special needs of the CV community


Time
-
evolving imagery


ECG and EP data


CV
-
specific vocabularies


Integration of multi
-
scale data sets


Specific data analysis workflows



Let the CV community drive technology development


NHLBI
-
FUNDED
Studies


Multi
-
Ethnic Study of Atherosclerosis


Coronary Artery Disease Risk in Young Adults


Minority Health Grid


Jackson Heart


Pediatric Heart Network


ECG Tool Initial Design/Workflow

Physionet Workflow




Reynolds Workflow




Data Storage
Services

Norav ECG Data
(RDT)

Physionet ECG Data

(WFDB


header, data)

ECG Data

Analytical
Services

ECG Analysis Parameters

Analysis
Results

Services

RDT
-
> HL7aECG

WFDB ECG Data

Reynolds ECG Analysis
Algorithms

Physionet ECG Analysis
Algorithms

Results

Results

Metadata XML

CVRG Web Interfaces: Initial Approach


Alpha CVRG Portal leveraged
caGrid

Portal and Web
Single Sign
-
On (
WebSSO
)


caGrid

Portal built upon
Liferay

4.1 open
-
source Portal Server


caGrid

WebSSO

used Java Architectures Special Interest Group
Central Authentication Service (JA
-
SIG CAS)


Portlets

implemented:


Beta Signup


ECG Storage/Analysis Workflow (end
-
to
-
end for both workflows)


Imaging Storage & Analysis


Heart shape and motion analysis


ProteinDB

utilization

Beta Signup/ECG Workflow Demo

Initial Approach Lessons Learned


Portal (e.g.,
Liferay

4.1)


All the work is done on the server


Changing the tabs requires a web browser refresh


Resets the
portlet

displayed so data entry starts all over again



New requirements appeared during development


Need to dynamically display and annotate an ECG


Dynamic refresh of
portlets

themselves difficult


Ability to display an embedded scrolling graph next to impossible


Call to tools outside of a
portlet

required extensions to
Liferay

itself


Portal environment customization should be minimized


Investigation of Web 2.0


Web 2.0 interfaces/tools


Work can be divided between the server & web browser


Components can be placed in web pages or executed standalone,
making changes dynamic



Yahoo User Interface (YUI)


Open
-
source JavaScript library


Used by i2b2 in Web Client



Google Web Toolkit & API Library (GWT)


Open
-
source Java project with
plugin

for Eclipse


Allows Java developers to produce rich JavaScript tools without
knowledge of syntax


Used by
LabKey

&
WebProtege


WFDB, HL7aECG

RDT, GE MUSE

ECG Tool Revised Design/Workflow

CVRG Web Interfaces: Revised Approach


Prototype ECG Gadget (renamed
ECGrid

Toolkit)


Built using GWT & Google Visualization API


Can exist in a portal, a web page, a dashboard, a flash drive
and/or a handheld device (e.g.,
iPhone
)


Expanded avenues of tool access, “putting it in the users’ hands”


Functions on multiple platforms and multiple browsers


Functionality implemented:


Integrated the ECG workflows into one unified workflow


Accepts multiple ECG formats stores in
Physionet’s

WaveForm

DataBase

(WFDB) format


Extended the capability of scrolling ECG visualization


Allows for annotation within the waveform, using National Center for
Biomedical Ontology (NCBO) REST Services real
-
time

Prototype ECGrid Toolkit Demo

Revised Approach Lessons Learned


Web 2.0 applications are more dynamic


Flexibility in deployment require development of
authorization/authentication components as well



Portal/Web 2.0 combination maximizes
strengths/minimizes weaknesses


Portal serves as an interface access point


Allows addition/removal of interfaces without a portal reboot


Interfaces can be run on servers separate from the portal


Appear centralized when they actually are distributed




Biopor
tal
Current CVRG Web Interfaces

XNAT
-
CVI

ECGrid

Toolkit

Galaxy

Web Data Services (JHU Cloud)

MR/CT/US

Analyses

Web Analysis Services

(Amazon EC2 & JHU Cloud)

ECG

Analyses

Ontology

(
RESTful

Web Service)

BioPortal
al

CVRG
Portal


Web
-
Browser

Software as a Service

Live Demonstration


CVRG Demonstration Portal


Galaxy


eXtensible

NeuroImaging

Toolkit


CV
Imaging (XNAT
-
CVI)


ECGrid

Toolkit


CVRG website
-
> Portal


http://www.cvrgrid.org

Future Development


In Process


Integration of NSF
Cybersecurity

Infrastructure Logon (
CILogon
)
into CVRG Portal


Alternative Shibboleth method developed using Johns Hopkins Enterprise
Authentication (for testing purposes)


Deployment of Survey
portlet

for user feedback on CVRG tools



Planned


Healthy Heart Imaging cohort to be made available to the
community for clinical trial controls via XNAT
-
CVI instance at Wake
Forest


ECGs

corresponding to Image datasets to be made available via
ECGrid

Toolkit
at Johns Hopkins


ECG analysis services to be made available via Galaxy, to
demonstrate workflow sharing and re
-
use

Web References


CVRG
-

http://www.cvrgrid.org/


JHU Institute for Computational Medicine


http://www.icm.jhu.edu/


Wake Forest University Image Lab


http://www.wakehealth.edu/imagelab/


Emory University Center for Comprehensive Informatics


http://cci.emory.edu/cms/index.html


University of Chicago Computation Institute
-

http://www.ci.anl.gov/


Liferay



http://www.liferay.com/community/welcome/dashboard


JA
-
SIG CAS
-

http://www.jasig.org/cas/


YUI
-

http://developer.yahoo.com/yui/


i2b2 Web Client
-

https://www.i2b2.org/


GWT
-

http://code.google.com/webtoolkit/


LabKey

-

https://www.labkey.org/


WebProtege

-

http://protegewiki.stanford.edu/index.php/WebProtege


NCBO
Bioportal



http://bioportal.bioontology.org/


Physionet



http://www.physionet.org/


CILogon

-

http://www.cilogon.org/







Acknowledgements

Johns Hopkins University

Michael
Miller

Raimond

Winslow

Laurent
Younes


Siamak

Ardekani

Stephen
Granite

David Hopkins

Kyle
Reynolds

Michael Shipway

Christian
Jurado

Emory University

Joel
Saltz

Andrew Post

Tahsin

Kurc

Richard Willard

Himanshu

Rathod

Wake Forest University

J. Jeffrey Carr

Yaorong

Ge

Ricardo
Peral

NHLBI R24 HL085343

NHLBI

Jennifer Larkin


University of Chicago

Ian Foster

Ravi
Madduri

Liu Bo