Post on 13-Jan-2016
Health-e-Child
Konstantin SkaburskasBased on presentations made by HeC partners
2 Health-e-Child 07. November 2006
• Establish Horizontal and Vertical integration of data, information and knowledge • Develop a grid-based biomedical information platform, supported by sophisticated and
robust search, optimisation, and matching techniques for heterogeneous information, • Build enabling tools and services that improve the quality of care and reduce its cost by
increasing efficiency• Integrated disease models exploiting all available information levels
• Database-guided decision support systems
• Large-scale, cross-modality information fusion and data mining for knowledge discovery
• A Knowledge Repository?
Project Objectives
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Instrument: Integrated Project (IP) of the Framework Program FP6
Project Identifier: IST-2004-027749
Coordinator: Siemens AG, Dr. Jörg Freund Partner: 14 European (companies, hospitals,
institutions) Timetable: 01-Jan-06 to 31-Dec-09 (4 years) Total cost: 16.7 Mio. € EC funding: 12.2 Mio. €
Web page: http://www.Health-e-Child.org
Project General Info
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GOSH
NECKER
UWE
CERN
IGG
SIEMENS
ASPER
UOA
INRIA
Project Map
LYNKEUS
UCL
EGFFGG
MAAT
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Clinical Context Diseases
• Heart diseases (Right Ventricle Overload, Cardiomyopathy), • Inflammatory diseases (Juvenile Idiopathic Arthritis), and • Brain tumours (Gliomas)
Clinical Institutions• I.R.C.C.S. Giannina Gaslini (IGG), Genoa, Italy • University College London, Great Ormond Street Children’s Hospital
(GOSH), London, UK • Assistance Publique Hopitaux de Paris – NECKER, Paris, France
Clinical Departments• Cardiology• Rheumatology• (Neuro-)Oncology• Radiology• Lab (Genetics, Proteomics, Lab)• Administration
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Data Integration Challenge (1)• 3 Hospital Nodes
• Integration of data stored in Hospital’s IS + fresh new data to be acquired
• Acquisition of large samples of Imaging data • 3 diseases X 300 cases X 2 modalities X 300 images
– i.e. at most 540000 images ~ 270 GB
• A Distributed Platform for sharing, manipulating and inferring data
• Decision Support System• Disease Modelling• Knowledge Discovery / Data Mining• Image Processing
• Automatic segmentation of right ventricle – to determine volume, ejection fractions etc for
cardiac MR and ultrasound images • Brain tumour segmentation/registration to determine
volume, location etc• Volume of synovial fluid in wrist MR scans
• Grid technology as the enabling infrastructureHeC Components
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• A1: Project Management
• WP1 – Project management
• A2: User Requirements Specifications
• WP2 – User requirements specifications
• A3: Ethical, Legal and Social Issues
• WP3 – Legal, ethical, and regulatory issues
• WP4 – Privacy and security
• A4: Platform Development, Vertical Data Integration and Knowledge Representation
• WP5 – Grid platform (Maat, CERN, UWE, Siemens)
• WP6 – Medical vertical knowledge representation
• WP7 – Data management layer and data integration mechanisms
• WP8 – Medical query processing• A5: Data Collection, Annotation and Knowledge Gathering
• WP9 – Data collection
• WP10 – Ground truth (annotated data) and clinical knowledge gathering
• A6: Disease Modelling, Decision Support and Knowledge Discovery based on Integrated Biomedical Information
• WP11 – Integrated disease modelling
• WP12 – Decision support systems
• WP13 – Biomedical knowledge discovery
• A7: System Integration
• WP14 – Deployment of the data management system and Grid gateway• A8: Dissemination Policy and Broader Impact
• WP15 – Training
• WP16 – Dissemination
Activities and Work Packages
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WP5 Objectives• To provide a Grid-aware infrastructure on which
the Health-e-Child applications can operate
• To develop appropriate APIs for applications to invoke Grid services
• To provide education to application developers on the use and operation of the Grid infrastructure
• To ensure that updates and releases of the Grid platform are available as the infrastructure evolves
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Challenges
• Security:• Strong authentication
• VOMS based authorization to all Grid resources
• Fine-grained data sharing/access. Granularity:• File
• DB views, tables, table rows
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Early Faced IssuesMainly Non-Functional since project has just started
• Selecting grid m/w services wrt project requirements• Lots of services/functionalities available• Different implementations with different levels of maturity
• Clustering grid m/w services• To reduce the h/w requirements & maintenance (1 server / Hospital)• To facilitate deployment (3 clinical sites + at least 5 institutional sites)
• Decentralisation of grid m/w services• Sites need to be as much as possible autonomous
• “Griddification” of Applications• Some of the HeC applications might be “gridified”
• Griddification has to be balanced against runtime and development complexity criteria
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Current Investigations• Selecting grid m/w services wrt project requirements
=> Services selection based on URS + Grid Questionnaire
• Clustering grid m/w services=> “Xenification” of OSs + clustering services wrt functionality
• Decentralisation of Grid Services=> Dependent on gLite developments, but already some possibilities with Master/Slave
configurations
• “Griddification” of Applications=> Introduced a classification of applications. Grid Questionnaire will certainly help in
making decisions
• Grid Access=> Abstracting grid access through dedicated service
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Remaining Challenges
• Data Integration in Hospitals (post phase 2)• What mechanisms to use? What will be the limitations (in particular with proprietary
systems?
• Patient Data Distribution & Sharing• What technology/implementation?
• Patient Image Files Sharing• Enabling the sharing of large files over the internet
• MRI @ GOSH = 500MB/patient• CT @ NECKER = 3.5GB/patient …raises bandwidth problems
• Griddification of Applications• Appears relevant for computation heavy algorithms or batch processing
• However many clinical algorithms have short runtime (e.g. image processing, since clinicians need almost instantaneous results)
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Non-functional Requirements• Hospital Sites should be autonomousautonomous
• Sites should not depend on any central services• Hardware requirements remain too high for Hospitals
• Getting access to the grid through one boxone box would be ideal• e.g. 1 Server per Hospital1 Server per Hospital
• Fine-grained security mechanism for accessing data (at the record level?)
Functional Requirements• PseudonymisationPseudonymisation as a native middleware service?• Native StreamingStreaming facilities for sharing large DICOM files• [ Native patient-centricpatient-centric data model(s)
• (flexibility) Optionally data model could be selected from existing standards (e.g. HL7…) or even created from scratch
• (interoperability) Optionally a native commodity for exporting/exposing data through different data models would be nice (model-driven)
• (interoperability) Optionally a data model (schema) discovery mechanism could help• Native connectors to external backends for batch data integration ]
1. Are HealthGridsHealthGrids likely to become the enabling infrastructure for Distributed PACSDistributed PACS?2. Is the GridGrid likely to become the enabling infrastructure for Knowledge RepositoriesKnowledge Repositories?
Middleware Requirements
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HeC Platform
HeC Server
GOSHHeC Server
Clinicians Laptops/Desktops
WorkstationIGG
NECKER
• One server per Hospital• Single entry point to HeC Platform
• One workstation per Department• For complex tasks a dedicated user dedicated user
interfaceinterface is used
• Generic computers on Intranet• Most functionalities accessible from
generic web browsersweb browsers
Clinician’sHeC Identity
Approach (1)
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HeC Platform Centralized
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HeC Platform DeCentralized
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Approach (2)• An intermediary access layer: the HeC Gateway
• To decouple client applications from the complexity of the grid and other computing resources
• Towards a platform independent implementation• Domain Specific Functionality exposed in the HeC Gateway• Grid mainly used as a Distributed & Federated PACS
• Different modalities of images to be anonymised and shared • Clinical Reports• Misc. Files
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Gateway Architecture
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Platform Use Cases
Local & GlobalRequires high responsiveness View Case
Global--Maintain Grid
Global--Knowledge Mining
Local & GlobalRequires high responsivenessFind Similarity
Local & GlobalRequires high responsivenessQuery
Local--Data Acquisition
Local & Global--Data Annotation
Global--Manage Sharing
Global--Maintain VO
Global--Maintain Tools
Local & Global--Maintain Information Schema
Local--Maintain Patient Database
3. Maintain Platform
Local & GlobalRequires high responsivenessUse Disease Models
Local & GlobalRequires high responsivenessUse Decision Support System
2. Retrieve & Exploit Information
1. Collect Information
ScopeComment(high-level) Use Case
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1st Technical Accomplishments
• Establishment of a Common Development Environment• Indispensible to synchronise partners and leverage synergy
• Creation of the Health-e-Child Virtual Organisation (VO)• Establishment of a Certificate Authority (55 certs delivered so far)• HeC VO (10 users) Structure in place, being tested
• 1st gLite Test-bed deployed in May 2006 on HeC dedicated servers• ~20 computers involved• Being refined according to project requirements
• HeC gateway (prototype version)• Authentication Client Application & Grid Service (VOMS enabled)• HeC Portal & Factory (exposing domain specific functionality)
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• What has been achieved, practically speaking?
• T4.2 Health-e-Child Certificate Authority• Redundant & Secured OpenCA Repositories
• 2 repositories synchronized by a USB stick• 1 repository exposing non-sensitive data• 1 repository installed in a secure computer
• 56 certificates delivered so far• Being used by all the services in the infrastructure from gLite to
gateway to common development environment
• T4.3 Security Prototype• Gateway service container and security policy in place• Authentication Client & Service
– Improved GSI & PKI model
• Logging Web-Portal– Featuring all facilities to browse gateway logs
» Can process statistics on gateway usage/reliability» Users Operations can be traced efficiently & real-time» Based on G
• LogAppender for Java– Asynchronous logger, therefore almost no computation cost– Log appended in a G DBMS
• VO Configured and under Test• Infrastructure Protected by Firewalls
– respecting the security rules defined for gateways
WP4 – Security & Privacy
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WP5 – Grid Platform
• What has been achieved?• T5.1 EGEE gLite Evaluation (M1-6 / 4MM)
• OK. Done via gLite Test-bed deployment at CERN & MAAT– Report should be appended to D5.1
• T5.2 Education / Training (M1-9 / 4MM)• OK. Done, undertaken several gLite tutorials until recently
• WP5 Team might be interested in having further technical tutorials
• T5.3 API Development (M6-12 / 10MM)• UP. API Information Collection completed
– Functionality wrapping is under process
• T5.4 gLite Test-bed (M9-15 / 14MM)• OK. First Test-bed, so-called « Roma »… demonstrated end May 2006
• 1 Central Site• 3 Local Sites (mimicking hospitals)
• T5.5 Prototype Testing (M15-18 / 3MM)• NS. However:
• Trying out some test suites for gLite
• Started Feedback to EGEE through CERN
• Milestones and Deliverables• D5.1 Report on delivered Grid prototype (due date: Month18)
• M5.1 Prototype Grid Platform (due date: Month18)
NS: Not Started yet
UP: OnGoing
OK: Done
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• What has been achieved, practically speaking?• T5.2 Education / Training
• 2006-02-27 gLite Tutorial @ CERN• 2006-09-26 gLite Tutorial @ CERN• 2006-10-10 gLite Tutorial @ CERN
• T5.3 API Development• Delivered HeC Infrastructure Requirements QuestionnaireHeC Infrastructure Requirements Questionnaire
• Collected all filled-in questionnaires (by 23-Oct. 2006)
• Questionnaires now have to be processed
• API integration scheme has been selected according to last tutorial results• API development has been split
• Already some embryo functionality can be tested through the HeC Shell (bundled in the Authentication Client Application for sysadmins)
• T5.1 & T5.4 gLite Test-bed• Test-bed, so-called « Roma »… demonstrated end May 2006• Test-bed now features:
• 1 Central site @CERN• 3 Hospital-like sites (2@CERN, 1@MAAT)• 1 Development G/W @ CERN
• For a total of 15 VMs~6 Servers15 VMs~6 Servers
WP5 – Grid Platform
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Infrastructure Outlook
Node dedicated to “Xenification” tests of gLite services. Temporary site, should disappear later.
OKCERN3 / 1Test SiteLocalCERN
Production Site
Production Site
Production Site
Development Site to train DSS connected to Grid
Mimicking a Hospital site. Could become a public Gateway for external clinicians/hospitals get access
Infrastructure should expand to 20 servers gradually
Mimicking a Hospital site. Temporary site, should disappear later.
Health-e-Child CA
Running core gLite services
Note
NSGOSHLondon
4 / 2Hospital SiteLocalGOSH
NSNECKERParis
4 / 2Hospital SiteLocalNECKER
NSIGGGenova
4 / 2Hospital SiteLocalIGG
OKMAAT Madrid
4 / 1Hospital / Development Site
LocalMAAT
UPMonth?
SIEMENSMunich
4 / 2Development SiteLocalSIEMENS
Computational Site
Hospital / Test Site
VO
VO
Sub-Type
UPMonth12
UWE Bristol
4 / 2LocalUWE
OKCERN2 / 2LocalCERN
OKCERN1 / 1CentralMAAT
OKCERN6 / 1CentralMAAT
StatusLocation# of VM / Servers
TypeOwner
WP5 – Grid Platform
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Health-e-Child 07, November 2006
WP14 – Connectivity Deployment
NS: Not Started yet
UP: OnGoing
OK: Done
• Milestones and Deliverables• D14.1 Report on Deployed Prototype (due date: Month18)
• What has been achieved?• UP. T14.1 Deployment of the Connection (M5-10 / 8MM)
• To speed up the process, MAAT is planning to: – 1. Order servers for Hospitals – 2. Batch install them– 3. Ship them to Hospitals and– 4. Finalize deployment onsite
• Currently preparing the deployment logistic– MAAT delivered recently Hospitals servers specs proposal– Deployment Team constituted and ready to proceed
• NS. T14.2 Linkage to DSS (M11-18 / 4MM)• NS. T14.3 Browsing of Data through Specified Ontologies (M11-18 / 2MM)
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Health-e-Child 07, November 2006
• What has been achieved, practically speaking?
• Test-bed used as a learning environment to perfect up-coming deployment• Deployment recently exercised through installation of a “Hospital-like” site
@ MAAT
• Server Pricing for Hospitals• Got proposal from DELL Spain (good prices ~ 1K€ lower than public prices)
• Deployment will be documented. Procedures are being properly described• Deployment Procedure Documentation• Hardware Test Report (1 per server delivered to Hospitals)
– For properly assessing the servers to be deployed in Hospitals• Software Test Report (1 per Hospital Site)
– For properly validating a site installation
• All Reports to be appended to D14.1
WP14 – Connectivity Deployment
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• What is planned?• Servers preparation phase to last 3 months (once orderedonce ordered)
• Targeted 1st Hospital: IGG (GOSH 2nd & Necker last)• Ideal Objective would be to order h/w before the end of November 2006
(Month11)• Deployment in Hospitals to start at Month12
• “Ideal” Objective is to deploy one Hospital before European Review (Month14)
• Where do you foresee problems, risks and/or delays?• WP14 Description not relevant for T14.2 & T14.3 (deserves amendment)• Deployment already delayed• Hardware deprecation – Servers should be ordered no later than December
2006• Servers integration in Hospitals
• What could be the counter measures to avoid the problems, risks and delays?• Amend WP14 for the DoW2• Order the h/w at Month11/12• Tight interaction with Hospitals’ IT Departments
• might require a pre-deployment visitpre-deployment visit at each Hospital
WP14 – Connectivity Deployment