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VPH NoE Study Group #2Barcelona, October 2010.
The VPH ToolKit: Evolution and Sustainability
Yves Martelli, Universitat Pompeu Fabra
On behalf of WP3 Partners
VPH NoE, 2010
VPH NoE ToolKitStudy Group #2 – Barcelona, October 2010
Presentation Outline
Introduction to the VPH ToolKit
The evolution of ToolKit activity Sustainability focus Community driven
Sustainability themes How can we have a lasting impact?
Summary
2VPH NoE Study Group #2Barcelona, October 2010.
The VPH ToolKit Vision
VPH aim: collaborative investigation of the human body as a single complex system integrative approach
The ToolKit refers to the… technologies methods and services
…needed to achieve this aim
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ToolKit Principles
NOT a monolithic entity Impossible in such a broad field
NOT a collection of isolated tools No use for tackling big problems
IT IS… Interoperating Systems Built around common standards Intended for workflow operation
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ToolKit Status 2010 0/4
toolkit.vph-noe.eu 5
VPH NoE Study Group #2Barcelona, October 2010.
ToolKit Status 2010 1/4
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ToolKit Status 2010 2/4
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ToolKit Status 2010 3/4
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ToolKit Status 2010 4/4
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ToolKit Evolution
But the ToolKit must evolve… Curated Usable, flexible, and interoperable … to provide a range of practical solutions … for clinicians and biomedical researchers … instead of starting from scratch
And be designed to outlive the VPH-NoE
VPH NoE Study Group #2Barcelona, October 2010.
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Approach to content provision in the ToolKit
Involvement of NoE, Exemplars, VPH-I…
Assessment of needs
Mapping of topics, project outputs
Sustainability and Legacy concepts
Standards development
Community-building
Community Strategy MeetingFebruary 2010
VPH NoE Study Group #2Barcelona, October 2010.
Importance of community
MAF, itk etc.
Sustainability attributes/themes
12
Sustainability
ToolKit Evolution (Community Strategy Meeting)
Themes/Concepts• Community• Ontology• Infrastructure• Standards• Ethico-legal• Documentation• Exploitation• Interoperability & workflow• Usability
Activities• Access & identity• Simulation• Visualisation• Data• Quality• Provenance• Protocol• Research & innovation• Tools & techniques• Interoperability & workflow
Sustainability
Themes?
Activities?
VPH NoE Study Group #2Barcelona, October 2010.
Sustainability matrix
13
Sustainability
VPH-I ARCH
Contributingto
VPH matrix
VPH
Weaknesses: Ontol; Access/ID
Strengths: Comm; Tools/interop
ARCH
ToolKit Evolution (Community Strategy Meeting)
VPH NoE Study Group #2Barcelona, October 2010.
Systematic approach sought
Incorporate training into ToolKit ‘Guideline’ documents
ToolKit components
Support with training activities (workshops etc.)
Which topics? Imaging
Others? – explore user workflows Software development, methodologies, testing, evaluation?
14
Sustainability through Training
ToolKit Evolution (Community Strategy Meeting)
VPH NoE Study Group #2Barcelona, October 2010.
NoE-wide effort
ToolKit provision
ToolKit hosting
ToolKit dissemination
A sustainable resource!…beyond the end of the project
…adequate infrastructureAccessible
Secure15
Sustainability through Dissemination
ToolKit Evolution (Community Strategy Meeting)
A VPH Portal?
VPH NoE Study Group #2Barcelona, October 2010.
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ToolKit WP: Legacy will be ToolKit content
Standards & Good Practice Guidelines
Mechanisms for dissemination
Adequate representation across all needs
Novel content in wider context
Working Groups – content and guidance
Allocated leads, members
Resulting Strategy
ToolKit Evolution (Community Strategy Meeting)
VPH NoE Study Group #2Barcelona, October 2010.
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Key Sustainability Themes
Standards Crucial for tool interoperability, and for sharing data and models
Ontologies Standard ontological annotation of models and data facilitates
interconnection of ToolKit resources
Certification Demonstrably high quality, well documented, and properly
validated
Interoperability and workflows Tools must be usable in tandem to achieve scientific and clinical
goals
User friendliness and relevance Last in the list, but of fundamental importance!
(Community Strategy Meeting)
VPH NoE Study Group #2Barcelona, October 2010.
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Activity UCL UOXF CNRS INRIA UPF UOA EBI USFD IMIM
Content - Categorised
Models TKL Yes Yes
Modelling Aids Yes Yes Yes TKL
Imaging Yes Yes TKL TKL TKL Yes Yes Yes
Data (non-imaging) Yes Yes Yes Yes TKL
Interactions Yes Yes Yes TKL Yes
Infrastructure TKL Yes
Ways of working Yes Yes Yes TKL
A Specialist for Every Specialty?
TKL: ToolKit Leader
ToolKit Evolution (Community Strategy Meeting)
Talk to us!VPH NoE Study Group #2Barcelona, October 2010.
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Underlying Requirements
Funding Variety of possible models
Community …of developers
…of users
Development processes Otherwise development becomes unwieldy
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Legacy will be ToolKit content Engagement to obtain and promote content
• Not just generating novel content
Guidelines & Good Practice
Mechanism for dissemination
Interoperability focus for development Standards-based
Training
Resulting ToolKit Strategy
VPH NoE Study Group #2Barcelona, October 2010.
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Guidelines for Good Practice
How do we obtain high quality content?
Share knowledge, be autodidacticE.g. How can we make good use of ontological annotation?
So: identification of 8 key Guidance Topics
Characterisation of tools, models, data
Annotation, Provenance, Licensing
Interoperability, Usability/Training
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Guideline Detail
All Guidelines share common structure Explanation of Guideline Topic: e.g. Tool Characterisation Underlying Concepts Interactions and Dependencies Applicable Legislation Standards and Standards Bodies Characteristics Methods of Verification Ownership Training Maintenance Ranking Documentation, Reporting Templates Further Information References
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Guideline Progress
All Guidelines drafted; release ~Q1 2011 Will be available via ToolKit Portal
Topic Lead Status Outline Draft 1First
Release
Tool Characterisation CNRS Refining characterisation criteria Q1-2011
Model Characterisation UOA Scope extensive, characterisation criteria complex Q2-2011
Data Characterisation INRIA Scope established, metadata/verification complex Q1-2011
Ontological Annotation EBI Concepts, standards and best practice, reference Q1-2011
Interoperability UPF Complex; seeking non-imaging input Q1-2011
EthLegal/Provenance USFD Advanced; issues: external standards, verification Q1-2011
Licensing UOXF Concepts, guide to choice, open source focus Q1-2011
Usability/Training UCL Importance, eval’n criteria, security mechanisms Q1-2011
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Already integrated into ToolKit Portal Relevant articles/advice provided
http://toolkit.vph-noe.eu/component/content/article/9
Open source licence advocated Considerations
• Approved by OSI; business friendly; license compatibility; attribution; legal jurisdiction
Acknowledged licenses• AGPL, Apache v2, 3-clause BSD, 4-clause BSD, CeCILL v2, CeCILL-B v2,
CeCILL-C v2, EUPL, GPL v2, GPL v3, LGPL v2.1, MIT, MPL v1.1
Licensing Guideline
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ToolKit Content
Sources: 5 key groups… Novel content
Exemplar projects
VPH-I projects
External sources
Coming soon: Associates
VPH NoE Study Group #2Barcelona, October 2010.
ToolKit: Novel Content
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Partner Activities Summary
UCL AHE/ACD/GS Hosting, security management and workflow support
UOXF Chaste/Environment Cardiac simulator and cell-model test environment
CNRS API, GUIDE DCM API and GUIDE
INRIA MedINRIA Data Fusion Interface; one-clicks; multi-platform; also API/GUIDE
UPF API, GUIDE (Gimias) DCM API and GUIDE
UOA OpenCMISS/cmgui/PMR2/CellML… Multiplicity of ML-based activities
EMBL API, Notation Anatomy API and Graphical Notation for Physiology
USFD Data content, environment Hospital data exposure system well-advanced
IMIM GPUGrid/Rboinc/Activ8/ADUN/ByoDyn Multiple molecular systems and tools in the ToolKit
VPH NoE Study Group #2Barcelona, October 2010.
ToolKit: Content from EPs
27
Activity Lead Summary ToolKit
Content - Exemplars
SeedEP1 (Art’l pressure) CNRS Core AP Model (CNRS) yielding Tools, Models and Data 2010
SeedEP2 (MSK model) ULB Musculoskeletal (ULB) yielding Tools, Models and Data 2011
SeedEP3 (Atherome) KI Vertical and horizontal Atherome: Models and Data 2010
SeedEP4 (Drug safety) IMIM Drug safety prediction: Tools, Models and Data Now
SeedEP5 (Brain function) ERCIM Modelling brain function: Tools and Models V Soon
EP6 (Guyton Annotation) EBI Ontologies for Data/Model interoperability: Data 2011
EPC2 #1: Genetics/Mscale Cigene Genetic theory & data with MS modelling 2012
EPC2 #2: Infrastructure USFD Infrastructure implementation, interaction with Call 6 2012
EPC2 #3: Imaging W/Flow CNRS Virtual Imaging Platform for workflows 2012
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Activity VPH-I Lead WP3 Status ToolKit
Content - VPH-I Projects
ARCH Mario Negri CNRS Negotiating content 2012
ARTreat Sword Tech USFD A challenging project… TBA
ContraCancrum FORTH UCL Workflow engine and workflow 2010/11
euHeart Philips UOA Multiplicity of ML models Now+
HAMAM Erasmus INRIA Image registration and data 2012
IMPPACT Fraunhofer CNRS Segmentation, reg’tion, mesh, vis’ation 2012
NeoMARK Uni-Hosp Parma UPF Database, data analysis tools 2011
PASSPORT IRCAD INRIA Segmented images, models, vistools… 2011
preDiCT UOXF UOXF VRE cardiac drug electro-simulation 2010/11
PredictAD VTT Finland EBI Negotiating content - ontological TBA
VPH2 Noema Life UCL Patient condition assessment 2010
VPHOP IO Rizzoli USFD Osteoporosis multi-outputs 2010/11
C4P1: RICORDO EBI EBI Detailed arrangements (WP3-led) 2011
C4P2: MSV @n/OP/IUPS UPF Multiscale vis extension to VTK (open) 2012+
C4P3: TUMOR CC/ACGT/NoE UOXF Initial stages TBA
C4P4: NMS Physiome OP/SimBIOS USFD Initial stages TBA
C4P5: Sim-e-child Health-e-Child UOXF Initial stages TBA
ToolKit: Content from VPH-I
VPH NoE Study Group #2Barcelona, October 2010.
ToolKit: External Content
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Activity Leads Status ToolKit
Content - Categorised
Models UOXF Many hundreds of models known… 2010+
Modelling Aids UOA Content available, approach being designed 2010+
Imaging CNRS/INRIA/UPF Much content known, strategy being defined 2010+
Data (non-imaging) USFD Several co-operations already in place 2010+
Interactions EBI 30+ identified, strategy developing 2010+
Infrastructure UCL Interactions with other management teams 2010+
Ways of working IMIM Strategy being developed; hand-over needed 2010+
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ToolKit Overall Statistics
With such a varied field, summaries are either over-simplistic or too long!
It’s non-trivial to give an indication of the effort involved in bringing different content to the ToolKit
Nevertheless, we need some indicator of progress
The next slide counts identified content…
Health Warning!Summarising the ToolKit can
make you question your sanity
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Count of content available via the ToolKit PortalN=Novel, M=Exemplars, V=VPH-I, T=External
Numbers for last year, this year and definite future items
ToolKit non-model items total 115Identified/developed models currently number around 480
ToolKit Overall Statistics
TotalsN M V T N M V T N M V T
Models UOXF 1 N/A
Modelling Aids UOA 6 2 2 9 2 2 2 7 1 33
Imaging CNRS/INRIA/UPF 1 1 1 1 1 1 6
Data (non-imaging)
USFD 2 1 3 1 1 2 1 5 16
Interactions EBI 1 1 2 1 20 25
Infrastructure UCL 2 2 2 2 1 4 1 14
Ways of working IMIM 8 13 21
Definite Future
Not counted – models exist only in separate repositories
Category ChampionLast Year (pre 1/9/09) This Year (1/9/09-1/9/10)
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ToolKit: Workflow View
Discipline Step1 Step2 Step3 Step4 Step5 Step6 Step… Last
@neurysm Image import
Format Convert
GAR Segment
Model Bounds
Vessel clip
Centre line
Mesh BCs
Tools… Tool 1 Tool 2 Tool 3 Tool 4 Tool 5 Tool 6 Tool 7 Tool N
Cardio 1
Tools…
Ortho 1
Tools…
Example: Image processing, by medical application
… a grid/graphical view of the GUIDE system
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ToolKit: Impact Views
Usage by research community
Usage in clinic
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VPH ToolKit Portal
http://toolkit.vph-noe.eu/
Main front-end for the VPH ToolKit
Registration opened to the public in September 2009 Advertised within VPH-I and at conferences
Submission rate increasing; now 58 entries
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ToolKit Dissemination
The current portal has limitations Limited integration with other VPH websites Need to be more community-centric Allow linked content, documents, etc. Integrated model & data hosting/provision Extend indications of tool interoperability Support for detailed curation
Need for a sustainable resource …beyond the end of the VPH-NoE …adequate infrastructure
VPH NoE Study Group #2Barcelona, October 2010.
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Summary – ToolKit Ambition
Sustainable – legacy to the community
Repository for Tools, Models, Data
Structured content, workflow-aligned
Contained in versatile portal
Supported by sophisticated infrastructure Working with Call 6 Infrastructure teams
Mechanism for continued evolution
VPH NoE Study Group #2Barcelona, October 2010.
VPH-NoE ToolKit Partners
# Partner Institution PM
1 UCL University College London 27
2 UOXF University of Oxford 48
3 CNRS Centre National de la Recherche Scientifique 30
5 INRIA Institut National de Recherche en Informatique et Automatique 30
7 UPF Universitat Pompeu Fabra 44
8 UOA University of Auckland 44
9 EMBL European Molecular Biology Laboratory 44
10 USFD University of Sheffield 44
12 IMIM Institut Municipal d'Investigació Mèdica 24
Total 335
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VPH-NoE ToolKit Team
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Peter?
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Question Time
The financial support of the European Commission is gratefully acknowledged. Material in this presentation reflects only the author's views and the Commissionis not liable for any use that may be made of the information contained herein.
VPH NoE, 2010.
Thank You
VPH NoE Study Group #2Barcelona, October 2010.
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