Structure

To meet the varied computational, design and infrastructure challenges, VPH-Share has divided its activities between a set of work packages. Share across the project's partners, these will each produce a distinct structural component, together supporting the VPH-Share process, from design to delivery.

Cloud platform

In the recent years medical scientists' abilities to produce complex data, such as scans and multicomponents time series, have tended to outstrip the ability to handle them effectively.  VPH-Share has developed a cloud computing platform with huge capacity, which enables users to share the vast amounts of complex data necessary to generate the Virtual Physiological Human. By consulting our flagship workflows, we determined how services can best be developed specifically for the needs of human modelling projects. The work is being held by CYFRONET.

The cloud platform will provide:

  • Resource allocation management dedicated to VPH application scenarios
  • An execution environment for flexible deployment of scientific software
  • Virtualised access to high performance execution environments
  • Cloud data access for very large objects and data transfer between services
  • Data reliability and integrity to ensure sound use of biomedical data
  • An appropriate security framework

 

Data management

With the large and growing level of biomedical information outrunning current information management practice, VPH-Share has also created a unified data management platform, which enables data controllers to manage patient information - images, records, diagnoses, treatment plans, outcomes - to suit their needs. Data sources include those from the @neurIST project - a rich data set of over 1200 images of cerebral aneurisms - and the NHS Information Centre including, for example, National Bowel cancer clinical audit data obtained from 100,000 patients over 8 years. The data infrastructure:

  • Exposes data services, de-identify selected data items and manage the data service on the cloud environment
  • Builds a service strcuture based on the renowed Vienna Grid Environment (VGE)
  • Creates data federation schemes across multiple data sources
  • Provides semantic mechanisms to discover, link and search data collections and services
  • Links data in personal health records to integrate in the data management platform

This work is being led by Sheffield Teaching Hospitals. 

Semantics

For VPH-Share resources to be meaningful to users, annotation must be consistent, irrespective of the data origin. VPH-Share uses semantic techniques to annotate resources, working with the data originators to determine appropriate semantic vocabularies. We use Semantic Web Services and state-of-the-art semantic algorithms to build an architecture sufficiently equipped to handle the complex data essential for the Virtual Physiological Human. Atos Origin is leading this work. The VPH-Share semantics:

  • Provides a coherent semantic architecture to ensure the content has a legacy
  • Provides a set of ontologies to describe the data in the project
  • Creates services to create, store, and retrieve metadata associated with any resource in the infostructure efficiently
  • Establishes an infrastructure for semantic web services to allow the annotation, selection, and invocation of services and workflows
  • Develops services to apply statistical or inference techniques, to provide additional information obtained from VPH-Share data

Patient avatar

To support the introduction of personalised multiscale models VPH-Share has developed the concept of the patiet avatar, the digital representation of each individual's personal medical information. Every patient has its own unique avatar, storing the raw material from which the physiology can be simulated, and VPH-Share is establishing a framework for the integration of this data, ultimately sufficient to drive any VPH simulation. Not all the data required for simulation can neccessarly be obtained by direct measurement (typically boundary conditions, such as pressure or flow, present difficulties), so the project is also devising techniques for parameter estimation, important not least when studying physiological extremes, such as heart attacks. To address these issues, VPH-Share:

  • Develops a process to formulate, analyse and annotate models
  • Develops the patient avatar using VPH mark-up languages
  • Applies and develops the tools for recognition of variation and uncertainty in data, model parameters and boundary conditions, and for the estimation of unknowns
  • Illustrates the power of this approach using four existing state-of-the-art personalised models, demonstrating how the predictive power of these models can be enhanced by proper assimilation of rich data sources

King's College London is leading this work. 

Portal 

VPH-Share has also developed the crucial visual element of the computational environment - the user interface, through which clinicians and researchers will access the content. This portal, the VPH-Share Master Interface, provides access to all available facilities and data as 'atomic' services - small perfectly - designed elements of the larger process. These services are available to use individually, or in any combination, providing all the necessary tools for the Virtual Physiological Human computational environment. Users are able to use information already implemented in the system, and freely introduce their own, allowing projects to share data and develop technologically through joint operation and international collaboration. The portal:

  • Integrates the services for the visualisation that will enrich the user experience
  • Develops and distribute VPH-Share atomic services
  • Develops the VPH-Share master interface
  • Describes and execute application workflows
  • Integrates existing workflows into the VPH-Share infostructure

University of Sheffield is leading this work.

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