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The VPH ToolKit: Evolution and Sustainability

VPH NoE ToolKit. Study Group #2 – Barcelona, October 2010. The VPH ToolKit: Evolution and Sustainability. Yves Martelli, Universitat Pompeu Fabra On behalf of WP3 Partners.  VPH NoE, 2010. Presentation Outline. Introduction to the VPH ToolKit The evolution of ToolKit activity

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The VPH ToolKit: Evolution and Sustainability

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

  2. 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 2 VPH NoE Study Group #2 Barcelona, October 2010.

  3. 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 3 VPH NoE Study Group #2 Barcelona, October 2010.

  4. 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 4 VPH NoE Study Group #2 Barcelona, October 2010.

  5. ToolKit Status 2010 0/4 toolkit.vph-noe.eu 5 VPH NoE Study Group #2 Barcelona, October 2010.

  6. ToolKit Status 2010 1/4 6 VPH NoE Study Group #2 Barcelona, October 2010.

  7. ToolKit Status 2010 2/4 7 VPH NoE Study Group #2 Barcelona, October 2010.

  8. ToolKit Status 2010 3/4 8 VPH NoE Study Group #2 Barcelona, October 2010.

  9. ToolKit Status 2010 4/4 9 VPH NoE Study Group #2 Barcelona, October 2010.

  10. 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 #2 Barcelona, October 2010.

  11. Community Strategy Meeting February 2010 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 VPH NoE Study Group #2 Barcelona, October 2010.

  12. ToolKit Evolution (Community Strategy Meeting) Sustainability • Importance of community • MAF, itk etc. • Sustainability attributes/themes • 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? 12 VPH NoE Study Group #2 Barcelona, October 2010.

  13. ToolKit Evolution (Community Strategy Meeting) Sustainability ARCH • Sustainability matrix Contributing to VPH matrix VPH VPH-I ARCH VPH NoE Study Group #2 Barcelona, October 2010. Strengths: Comm; Tools/interop Weaknesses: Ontol; Access/ID

  14. ToolKit Evolution (Community Strategy Meeting) Sustainability through Training • 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? VPH NoE Study Group #2 Barcelona, October 2010.

  15. ToolKit Evolution (Community Strategy Meeting) Sustainability through Dissemination • NoE-wide effort • ToolKit provision • ToolKit hosting • ToolKit dissemination • A sustainable resource! • …beyond the end of the project • …adequate infrastructure • Accessible • Secure A VPH Portal? VPH NoE Study Group #2 Barcelona, October 2010.

  16. ToolKit Evolution (Community Strategy Meeting) Resulting Strategy • 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 VPH NoE Study Group #2 Barcelona, October 2010.

  17. Key Sustainability Themes (Community Strategy Meeting) • 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! VPH NoE Study Group #2 Barcelona, October 2010.

  18. ToolKit Evolution (Community Strategy Meeting) A Specialist for Every Specialty? Talk to us! TKL: ToolKit Leader VPH NoE Study Group #2 Barcelona, October 2010.

  19. Underlying Requirements • Funding • Variety of possible models • Community • …of developers • …of users • Development processes • Otherwise development becomes unwieldy VPH NoE Study Group #2 Barcelona, October 2010.

  20. Resulting ToolKit Strategy • 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 VPH NoE Study Group #2 Barcelona, October 2010.

  21. Guidelines for Good Practice • How do we obtain high quality content? • Share knowledge, be autodidactic • E.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 VPH NoE Study Group #2 Barcelona, October 2010.

  22. 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 VPH NoE Study Group #2 Barcelona, October 2010.

  23. Guideline Progress • All Guidelines drafted; release ~Q1 2011 • Will be available via ToolKit Portal VPH NoE Study Group #2 Barcelona, October 2010.

  24. Licensing Guideline • 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 VPH NoE Study Group #2 Barcelona, October 2010.

  25. ToolKit Content • Sources: 5 key groups… • Novel content • Exemplar projects • VPH-I projects • External sources • Coming soon: Associates VPH NoE Study Group #2 Barcelona, October 2010.

  26. ToolKit: Novel Content VPH NoE Study Group #2 Barcelona, October 2010.

  27. ToolKit: Content from EPs VPH NoE Study Group #2 Barcelona, October 2010.

  28. ToolKit: Content from VPH-I VPH NoE Study Group #2 Barcelona, October 2010.

  29. ToolKit: External Content VPH NoE Study Group #2 Barcelona, October 2010.

  30. ToolKit Overall Statistics Health Warning! Summarising the ToolKit can make you question your sanity 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… VPH NoE Study Group #2 Barcelona, October 2010.

  31. ToolKit Overall Statistics Unhelpful Count of content available via the ToolKit Portal N=Novel, M=Exemplars, V=VPH-I, T=External Numbers for last year, this year and definite future items ToolKit non-model items total 115 Identified/developed models currently number around 480 VPH NoE Study Group #2 Barcelona, October 2010.

  32. ToolKit: Workflow View Example: Image processing, by medical application … a grid/graphical view of the GUIDE system VPH NoE Study Group #2 Barcelona, October 2010.

  33. ToolKit: Impact Views • Usage by research community • Usage in clinic VPH NoE Study Group #2 Barcelona, October 2010.

  34. 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 VPH NoE Study Group #2 Barcelona, October 2010.

  35. 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 #2 Barcelona, October 2010.

  36. 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 #2 Barcelona, October 2010.

  37. VPH-NoE ToolKit Partners VPH NoE Study Group #2 Barcelona, October 2010.

  38. VPH-NoE ToolKit Team Peter? ??? ??? VPH NoE Study Group #2 Barcelona, October 2010.

  39. Question Time Thank You 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 Study Group #2 Barcelona, October 2010.  VPH NoE, 2010.

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