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The Virtual Physiological Human ToolKit

All Hands Meeting 2009. Oxford – 8 th December 2009. The Virtual Physiological Human ToolKit. Jonathan Cooper University of Oxford On behalf of the ToolKit team.  VPH NoE, 2009. The VPH ToolKit Vision. VPH aim: collaborative investigation of the human body as a single complex system

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The Virtual Physiological Human ToolKit

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  1. All Hands Meeting 2009 Oxford – 8th December 2009. TheVirtual Physiological HumanToolKit Jonathan Cooper University of Oxford On behalf of the ToolKit team  VPH NoE, 2009

  2. 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. Who is in the VPH? Parallel VPH projects Industry Grid access CA CV/Atheroschlerosis IP Liver surgery STREP Breast cancer/ diagnosis STREP Heart/LVD surgery STREP Osteoporosis IP Oral cancer/BM D&T STREP Networking NoE Cancer STREP Heart/CV disease STREP Vascular/AVF & haemodialysis STREP Liver cancer/RFA therapy STREP Heart/CV disease STREP Alzheimer's/BM & diagnosis STREP Security and Privacy in VPH CA Other Clinics

  4. Why does the VPH community need a ToolKit ? • Much excellent research already done on individual components • But much repetition too • Need for greater collaboration and interoperability to achieve greater scientific breakthroughs

  5. So what is a VPH ToolKit? Grid access & middleware Simulation Tools Workflow environments Image Analysis Tools Data Fusion Ontologies VPH markup languages for model encapsulation VPH markup languages for data encapsulation Model Repositories Data Repositories

  6. So what is a VPH ToolKit?

  7. VPH NoE: data activities • Looking at wide exposure of clinical data • What is allowed: ethical issues • Implementation: Local & global infrastructure needs • Data standards required in order to make use of it • DICOM, HL7, etc.

  8. VPH model reuse requirements • What is needed to reuse published models? • Minimum information standards • MIRIAM, MIASE • Syntax • SBML, CellML, FieldML, NeuroML, … • SED-ML • Semantics • Metadata • Ontological annotation

  9. VPH ontology use 9

  10. VPH ToolKit: The Challenge • Many tools, services & technologies are available to assist with VPH research • Hard to know what is available • Hard to learn from experiences of others • Especially when crossing academic disciplines

  11. The VPH ToolKit Portal • A database of VPH research-related ‘capacities’ • Specific tools • Methods for conducting VPH research in an integrative fashion • Services available to researchers • Also some articles on relevant topics • Facility to submit new entries, and reviews • These are moderated by the NoE at present

  12. Next steps • Increased community engagement • Seeking contributions to the ToolKit • Training activities • Putting the pieces together • e.g. providing examples of integrating tools, centred around scientific workflows

  13. Any questions? http://toolkit.vph-noe.eu/ 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, 2009

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