Health-e-Child Konstantin Skaburskas Based on presentations made by HeC partners

2Health-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

3Health-e-Child 07. November 2006  Instrument:Integrated Project (IP) of the Framework Program FP6  Project Identifier:IST  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: Project General Info

4Health-e-Child 07. November 2006 GOSH NECKER UWE CERN IGG SIEMENS ASPER UOA INRIA Project Map LYNKEUS UCL EGF FGG MAAT

5Health-e-Child 07. November 2006 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

6Health-e-Child 07. November 2006 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 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 infrastructure HeC Components

7Health-e-Child 07. November 2006 Data Integration Challenge (2) Heterogeneous Data/Imaging Sources DB Backends: from simple MS ACCESS to complex Patient Information Systems like TOMCAT, RIS … No or few linkage bw department’s IS Various imaging modalities: MRI, CT, US, X-Ray… Various imaging devices: Siemens Bi-Plan, GE Vivid7, Sequoia, HP128… Heterogeneous Connectivity PACS not yet present in all Hospitals/Departments Hospitals have different Hardware/Network/Security constraints A 3-Phase Data Integration Scheme 1 st : A temporary offline data acquisition application 2 nd : An online data acquisition application (interacting with the platform) 3 rd : A background data integration service (in the platform)

8Health-e-Child 07. November 2006 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

9Health-e-Child 07. November 2006 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

10Health-e-Child 07. November 2006 Challenges Security: Strong authentication VOMS based authorization to all Grid resources Fine-grained data sharing/access. Granularity: File DB views, tables, table rows

11Health-e-Child 07. November 2006 Early Faced Issues Mainly 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

12Health-e-Child 07. November 2006 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

13Health-e-Child 07. November 2006 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 GOSH = 500MB/patient 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)

14Health-e-Child 07. November 2006 Non-functional Requirements autonomous Hospital Sites should be autonomous Sites should not depend on any central services Hardware requirements remain too high for Hospitals one box Getting access to the grid through one box would be ideal 1 Server per Hospital e.g. 1 Server per Hospital Fine-grained security mechanism for accessing data (at the record level?) Functional Requirements Pseudonymisation Pseudonymisation as a native middleware service? Streaming Native Streaming facilities for sharing large DICOM files patient-centric [ Native patient-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 ] HealthGridsDistributed PACS 1. Are HealthGrids likely to become the enabling infrastructure for Distributed PACS? GridKnowledge Repositories 2. Is the Grid likely to become the enabling infrastructure for Knowledge Repositories? Middleware Requirements

15Health-e-Child 07. November 2006 HeC Platform HeC Server GOSH HeC Server Clinicians Laptops/Desktops Workstation IGG NECKER One server per Hospital Single entry point to HeC Platform One workstation per Department dedicated user interface For complex tasks a dedicated user interface is used Generic computers on Intranet web browsers Most functionalities accessible from generic web browsers Clinician’s HeC Identity Approach (1)

16Health-e-Child 07. November 2006 HeC Platform Centralized

17Health-e-Child 07. November 2006 HeC Platform DeCentralized

18Health-e-Child 07. November 2006 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

19Health-e-Child 07. November 2006 Gateway Architecture

20Health-e-Child 07. November 2006 Platform Use Cases Local & GlobalRequires high responsivenessView 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

21Health-e-Child 07. November st 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)

22Health-e-Child 07. November 2006 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

23Health-e-Child 07. November 2006 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 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

24Health-e-Child 07. November 2006 What has been achieved, practically speaking? T5.2 Education / Training gLite CERN gLite CERN gLite CERN T5.3 API Development HeC Infrastructure Requirements Questionnaire Delivered HeC 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 3 Hospital-like sites 1 Development CERN 15 VMs~6 Servers For a total of 15 VMs~6 Servers WP5 – Grid Platform

25Health-e-Child 07. November 2006 Infrastructure Outlook Node dedicated to “Xenification” tests of gLite services. Temporary site, should disappear later. OKCERN3 / 1Test SiteLocalCERN 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 NSGOSH London 4 / 2Hospital SiteLocalGOSH NSNECKER Paris 4 / 2Hospital SiteLocalNECKER NSIGG Genova 4 / 2Hospital SiteLocalIGG OKMAAT Madrid 4 / 1Hospital / Development Site LocalMAAT UP Month? SIEMENS Munich 4 / 2Development SiteLocalSIEMENS Computational Site Hospital / Test Site VO Sub-Type UP Month12 UWE Bristol4 / 2LocalUWE OKCERN2 / 2LocalCERN OKCERN1 / 1CentralMAAT OKCERN6 / 1CentralMAAT StatusLocation# of VM / Servers TypeOwner WP5 – Grid Platform

26Health-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)

27Health-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” 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

28Health-e-Child 07, November 2006 What is planned? once orderedServers preparation phase to last 3 months (once ordered) Targeted 1st Hospital: IGG (GOSH 2 nd & 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 pre-deployment visitmight require a pre-deployment visit at each Hospital WP14 – Connectivity Deployment