VPH NoE Study Group #2 Barcelona, October 2010. The VPH ToolKit: Evolution and Sustainability Yves Martelli, Universitat Pompeu Fabra On behalf of WP3

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


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


ToolKit Status 2010 0/4

toolkit.vph-noe.eu 5










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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


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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


Importance of community

MAF, itk etc.

Sustainability attributes/themes

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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?


Sustainability matrix

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Sustainability

VPH-I ARCH

Contributingto

VPH matrix

VPH

Weaknesses: Ontol; Access/ID

Strengths: Comm; Tools/interop

ARCH



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?

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Sustainability through Training



NoE-wide effort

ToolKit provision

ToolKit hosting

ToolKit dissemination

A sustainable resource!…beyond the end of the project

…adequate infrastructureAccessible

Secure15

Sustainability through Dissemination


A VPH Portal?


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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



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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)


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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


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


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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


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


ToolKit: Content from EPs

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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


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


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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 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


VPH-NoE ToolKit Team

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Peter?


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


Documents

VPH NoE Study Group #2 Barcelona, October 2010. The VPH ToolKit: Evolution and Sustainability Yves Martelli, Universitat Pompeu Fabra On behalf of WP3