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Coarse-Grained Interoperability Scenarios in SHIWA: Challenges and Applications

Explore CGI goals, challenges, pilot applications in neuroscience, surface chemistry, medical simulation, bioinformatics, and scenarios like DTI Atlas, FSL BedpostX, GATE, and execution on SSP. Learn about successful implementation and discussions on meta-workflows in SHIWA.

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Coarse-Grained Interoperability Scenarios in SHIWA: Challenges and Applications

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  1. Coarse Grained Interoperability scenarios SHIWA SA2 presented by Vladimir Korkhov, AMC

  2. SHIWA Use Cases • Use case A: Running non-native workflows • Use case B: Creating and running meta-workflows • Use case C: Running workflows on multiple DCIs Coarse grained interoperability (CGI): Use cases A and B SHIWA CGI scenarios, Vladimir Korkhov, 11.04.2011

  3. Coarse-grained interoperability • Nesting of different workflow systems to achieve interoperability of execution frameworks SHIWA CGI scenarios, Vladimir Korkhov, 11.04.2011

  4. CGI goals • Meta-workflow – combination of heterogeneous native and non-native workflows • Creating a meta-workflow by encapsulating nested workflows to: • Utilize resources from different DCIs together (thus get more resources) • Combine workflows described in different languages and running on different engines • Be able to reuse workflows as a component in meta-workflows SHIWA CGI scenarios, Vladimir Korkhov, 11.04.2011

  5. CGI challenges • Construction of a meta-workflow • combining heterogeneous workflows • description of meta-workflows • Executing heterogeneous workflows • Accessing multiple DCI resources • Data transfers between DCIs • Security and credentials handling between DCIs SHIWA CGI scenarios, Vladimir Korkhov, 11.04.2011

  6. Pilot applications • Neuroscience • Surface chemistry • Medical simulation • Bioinformatics SHIWA CGI scenarios, Vladimir Korkhov, 11.04.2011

  7. Scenario 1: DTI Atlas • Neuroscience, brain imaging • Magnetic Resonance Imaging (MRI) • Diffusion Tensor MRI (DTI) • MR-modality enabling the identification of the orientation of human tissue. • Indirect measure of water diffusion in brain tissue • used in comparative studies of brain diseases that are thought to cause local damage to brain tissue • DTI Atlas:single average tensor field is computed for a group of subjects, which can then be used for further analysis. • CGI scenario: • Combine a pipeline workflow of sub-workflows performing separate analysis steps • re-use existing workflows SHIWA CGI scenarios, Vladimir Korkhov, 11.04.2011

  8. DTI Atlas implementation Co-registration MOTEUR/Dutch Grid Warping MOTEUR/Dutch Grid Fitting MOTEUR/Dutch Grid SHIWA CGI scenarios, Vladimir Korkhov, 11.04.2011

  9. Scenario 2: FSL BedpostX • Neuroscience, brain imaging • FMRIB Software Library (FSL) • BedpostX • Diffusion Tensor Imaging (DTI) • Magnetic Resonance Imaging (MRI). • reconstructs the fibers in each voxel using an advanced method that supports crossing fibers • CGI scenario: • Run on different DCIs in parallel to get more resources • Use implementations of the same workflow supported by different WF engines on different DCIs SHIWA CGI scenarios, Vladimir Korkhov, 11.04.2011

  10. FSL-BedpostX MOTEUR/Dutch Grid GWES/D-Grid FSL-BedpostX FSL BedpostX implementation SHIWA CGI scenarios, Vladimir Korkhov, 11.04.2011

  11. Scenario 3: GATE • Medical simulation • GATE • simulation software developed by the OpenGate Collaboration • http://opengatecollaboration.healthgrid.org • used here for radio- and hadrontherapy simulations, but it can also simulate image acquisition, e.g., Positron Emission Tomography. • CGI scenario: • Integrating heterogeneous workflows into the native workflow to achieve better performance by accessing different DCIs via workflow engines. SHIWA CGI scenarios, Vladimir Korkhov, 11.04.2011

  12. GATE implementation MOTEUR/EGI MOTEUR/EGI GWES/D-Grid SHIWA CGI scenarios, Vladimir Korkhov, 11.04.2011

  13. Execution on SSP • SSP – SHIWA Simulation Platform • SSP provides the means to: • Compose meta-workflows • Enact meta-workflows • Monitor meta-workflows execution • Retrieve results of the execution SHIWA CGI scenarios, Vladimir Korkhov, 11.04.2011

  14. Discussion • Construction of meta-workflows • Execution of meta-workflows • Multiple DCIs: access and execution • data transfers between DCIs, • multi-grid credential management • software dependencies • merge sub-workflows output results SHIWA CGI scenarios, Vladimir Korkhov, 11.04.2011

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