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UCSD / BIRN Coordinating Center NAMIC Group

UCSD / BIRN Coordinating Center NAMIC Group. Site PI: Mark H. Ellisman Site Project Lead: Jeffrey S. Grethe. Faculty Mark Ellisman Jeffrey Grethe Grid Application Development Integration of Slicer3 Execution model with Grid infrastructure Marco Ruiz Algorithm Development

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UCSD / BIRN Coordinating Center NAMIC Group

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  1. UCSD / BIRN Coordinating CenterNAMIC Group Site PI: Mark H. Ellisman Site Project Lead: Jeffrey S. Grethe

  2. Faculty Mark Ellisman Jeffrey Grethe Grid Application Development Integration of Slicer3 Execution model with Grid infrastructure Marco Ruiz Algorithm Development N-Channel Automated Colocalization Analysis Portal Development Integration of Slicer / NA-MIC Toolkit components w/ User Portal Ramil Manansala Application Integration Integration of NA-MIC Toolkit with BIRN environment Vicky Rowley Systems Support Support for NA-MIC components of BIRN grid Bao Nguyen Who are we – people

  3. What do we contribute - Collaboration • Provide collaborative portal environment • Enable researchers to store and interact with large collections of federated data within a distributed data grid

  4. What do we contribute - Algorithm Development • N-Channel Automated Colocalization Analysis • Quantitative tools to assess the co-distributions of molecular markers within individual cells and immuloabeled tissue slices. • Colocalization and spatial distribution analysis module within Slicer3

  5. Incorporating Microscopy Processing and Analysis Into 3-D Slicer Slice view Surface view • File readers to deal with variety of image file formats generated at NCMIR • Developing Slicer interface for existing tools used by NCMIR researchers (eg. IMOD, TxBR, etc) • Create a single, user-friendly application to unify image processing, visualization, analysis and annotation

  6. Grid Execution Module What do we contribute - Grid Computation • Provide researchers with customizable access to a computing environment that takes advantage of Grid-based infrastructures • Heterogeneous collection of arge scale compute resources are available to NA-MIC researchers and users of the NA-MIC kit (e.g. BIRN, TeraGrid, local clusters) • Provide interface module (Grid Wizard Interface) for the NA-MIC kit to enable distributed execution of algorithms from Slicer and modules such as BatchMake

  7. A Researcher’s “Grid” • A researcher’s high performance computing resource is usually a collection of resources (i.e. clusters) • To use this collection of resources, the “Client” is responsible to provide the logic to integrate the the disparate clusters within the logic of their specific applications • Most of the times this effort is non-trivial, non-reusable, non-extensible, lacks robustness and is far from giving the end user all the desired functionality

  8. “Grid Wizard Enterprise” enabled Cluster • Tight integration with cluster internals and transparent access to them. • Granular level of execution control: submission, pause, resume, abort. • Real time monitoring and alerting capabilities. • Granular reporting of historic, diagnostics and statistics data. • Transparent environment translation for requests. • Programmatic control with rich and simple API.

  9. Tool Integration - Generic: Slicer3

  10. Immediate Goals June 2008 February 2008 April 2008 Current On-Going: BatchMake Integration Grid Interface prototype Pre-release. Alpha version of complete infrastructure including automatic deployment Pre-release (Beta version) - Full Slicer 3 Integration Production Release - Stable version with drivers for most popular cluster components (including full transparent SRB support), full monitoring, alert capabilities and API bundles.

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