MIASGrid

1
MIAS-Grid

• Chris Rose, Katy Wolstencroft, Daniele Turi, Alan
  Williams, Chris Taylor (University of Manchester)
• Andrew Todd-Pokropek (UCL)

2
Talk Outline

• Chris Rose
• What is MIAS?
• Medical image and signal interpretation
• TODO
• Katy Wolstencroft
• myGrid platform workflows
• project status

3
What is MIAS?

• Medical Images and Signals
• Interdisciplinary research consortium
• Manchester, Oxford, UCL, Imperial
• From medical images and signals to clinical
  information
• 6-year project, just over half-way through
• MIAS-Grid is one of the e-Science components

4
Project Objectives

• e-Science workbench for medical imaging research
• virtual organisation - MIAS IRC
• distributed repository - discovery
• myGrid platform
• integrated workbench
• semantic grid technology - ontologies
• support for workflows

5
Image and Signal Interpretation

• HiRes/3D/Time
• Population-based studies
• Groundtruth annotation
• Computationally expensive
• Complex workflows

6
Collaborative Research

• Dispersed data algorithms
• Clinical metadata
• Ethical use/reuse
• Information management
• discovery, provenance, workflow

7
Quantitative Evaluation

• Researchers need to evaluate their image and
  signal interpretation algorithms
• Often no standard criteria (no standard data)
• Repeatability (need the same data)
• Effective data sharing enables quantitative
  evaluation

8
Data Sharing

• Currently ad hoc (e.g. over the desk)
• Ethical, legal and clinical governance issues
• patient confidentiality - security and encryption
• patient consent (who can do what with data)
• Issues of good clinical practice
• audit/provenance

9
Distributed Computation

• Image signal interpretation algorithms are
  computationally expensive
• Desire to offload/parallelise processing
• Covered later by Katy

10
Proposed Solutions

• Distributed repository of medical image signal
  data
• Semi-automatic population of repository from
  DICOM headers (A. Williams)
• Develop principled approaches to provenance (D.
  Turi)
• myGrid middleware Taverna workflows (Katy)

11
Distributed Repository

• XHTML Portal
• ontological description, search, administration
• Descriptions, files collections assigned URNs
• Distributed, redundant storage component
• Data upload and download clients
• Command line GUI Java apps

12
Example Use Case

• Demonstrate functionality through use cases
• Group-wise non-rigid registration of MR brain
  images
• managing image annotation data
• parallelising an expensive optimisation (workflow)

13
myGrid

• A suite of loosely-coupled components to allow
  users to construct, manage and publish in silico
  experiments
• Workflow design and enactment
• Distributed computing
• Provenance data management

14
myGrid Information Model
Applications
15
myGrid Use Cases
16
myGrid Workbench Taverna
17
User Community Differences
18
Data Differences
19
Application Extensions
20
myGrid Evolution

• Integrative biology project
• long-running workflows for simulations
• checkpointing
• Computing power (North West Grid)
• space for installing and running services
• Iteration, scheduling, failover
• can already do this with Taverna

21
Project Objectives

• Use myGrid platform to
• support sharing of algorithms data
• support research best practices
• Create a distributed repository for image, signal
  and related data
• Analyse scaling results to support wider community

22
Progress

• Ontology design
• MR imaging protocol
• knees study - vertical slice
• Distributed repository architecture
• Structured engagement with myGrid

23
Acknowledgements

• Funded by EPSRC as part of the MIAS-IRC project
  From Medical Signals and Images to Clinical
  Information (EPSRC GR/N14248/01) and UK Medical
  Research Council Grant No. D2025/31
• myGrid developers - EPSRC
• Tim Cootes - MIAS IRC
• AstraZeneca

24
Any Questions?
25
myGrid Background

• Middleware for in silico experiments in biology
• EPSRC e-science pilot project (2001-2005)
• Manchester, Newcastle, Sheffield, Southampton,
  Nottingham, EBI and RFCGR industrial partners
• New myGrid platform grant form June 2005
• Big user community - more than 1500 downloads

26
Related Work

• e-Diamond
• IXI
• MIAKT